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Published work

145 published item(s)

preprint2026arXiv

Breaking Dual Bottlenecks: Evolving Unified Multimodal Models into Self-Adaptive Interleaved Visual Reasoners

Recent unified models integrate multimodal understanding and generation within a single framework. However, an "understanding-generation gap" persists, where models can capture user intent but often fail to translate this semantic knowledge into precise pixel-level manipulation. This gap results in two bottlenecks in anything-to-image task (X2I): the attention entanglement bottleneck, where blind planning struggles with complex prompts, and the visual refinement bottleneck, where unstructured feedback fails to correct imperfections efficiently. In this paper, we propose a novel framework that empowers unified models to autonomously switch between generation strategies based on instruction complexity and model capability. To achieve this, we construct a hierarchical data pipeline that constructs execution paths across three adaptive modes: direct generation for simple cases, self-reflection for quality refinement, and multi-step planning for decomposing complex scenarios. Building on this pipeline, we contribute a high-quality dataset with over 50,000 samples and implement a two-stage training strategy comprising SFT and RL. Specifically, we design step-wise reasoning rewards to ensure logical consistency and intra-group complexity penalty to prevent redundant computational overhead. Extensive experiments demonstrate that our method outperforms existing baselines on X2I, achieving superior generation fidelity among simple-to-complex instructions. The code is released at https://github.com/WeChatCV/Interleaved_Visual_Reasoner.

preprint2026arXiv

Continuous Latent Diffusion Language Model

Large language models have achieved remarkable success under the autoregressive paradigm, yet high-quality text generation need not be tied to a fixed left-to-right order. Existing alternatives still struggle to jointly achieve generation efficiency, scalable representation learning, and effective global semantic modeling. We propose Cola DLM, a hierarchical latent diffusion language model that frames text generation through hierarchical information decomposition. Cola DLM first learns a stable text-to-latent mapping with a Text VAE, then models a global semantic prior in continuous latent space with a block-causal DiT, and finally generates text through conditional decoding. From a unified Markov-path perspective, its diffusion process performs latent prior transport rather than token-level observation recovery, thereby separating global semantic organization from local textual realization. This design yields a more flexible non-autoregressive inductive bias, supports semantic compression and prior fitting in continuous space, and naturally extends to other continuous modalities. Through experiments spanning 4 research questions, 8 benchmarks, strictly matched ~2B-parameter autoregressive and LLaDA baselines, and scaling curves up to about 2000 EFLOPs, we identify an effective overall configuration of Cola DLM and verify its strong scaling behavior for text generation. Taken together, the results establish hierarchical continuous latent prior modeling as a principled alternative to strictly token-level language modeling, where generation quality and scaling behavior may better reflect model capability than likelihood, while also suggesting a concrete path toward unified modeling across discrete text and continuous modalities.

preprint2026arXiv

Forbidden second harmonics in centrosymmetric bilayer crystals

Optical spectroscopy based on second-order nonlinearity is a critical technique for characterizing two-dimensional (2D) crystals as well as bioimaging and quantum optics. It is generally believed that second-harmonic generation (SHG) in centrosymmetric crystals, such as graphene and other bilayer 2D crystals, is negligible without externally breaking the inversion symmetry. Here, we show that with a new homodyne detection technique, we can apparently circumvent this symmetry-imposed constraint and observe robust SHG in pristine centrosymmetric crystals, without any symmetry-breaking field. With its exceptional sensitivity, we resolve polarization-resolved SHG in bilayer hexagonal boron nitride (h-BN), bilayer 2H-WSe$_2$, and remarkably, Bernal-stacked bilayer graphene, allowing us to unambiguously identify the crystallographic orientation in these crystals via SHG for the first time. We also demonstrate that the new technique can be used to non-invasively detect uniaxial strain and optical geometric phase in these crystals. The observed SHG in our experiments is attributed to second-order nonlinearity in the quadrupole channel, which is controlled by the presence of the $C_2$ symmetry instead of the inversion symmetry. Our new technique expands the capability of nonlinear optical spectroscopy to encompass a large class of centrosymmetric materials that could never be measured before, and can be used for quantum sensing of moiré materials and twisted epitaxial films.

preprint2026arXiv

GeoReason: Aligning Thinking And Answering In Remote Sensing Vision-Language Models Via Logical Consistency Reinforcement Learning

The evolution of Remote Sensing Vision-Language Models(RS-VLMs) emphasizes the importance of transitioning from perception-centric recognition toward high-level deductive reasoning to enhance cognitive reliability in complex spatial tasks. However, current models often suffer from logical hallucinations, where correct answers are derived from flawed reasoning chains or rely on positional shortcuts rather than spatial logic. This decoupling undermines reliability in strategic spatial decision-making. To address this, we present GeoReason, a framework designed to synchronize internal thinking with final decisions. We first construct GeoReason-Bench, a logic-driven dataset containing 4,000 reasoning trajectories synthesized from geometric primitives and expert knowledge. We then formulate a two-stage training strategy: (1) Supervised Knowledge Initialization to equip the model with reasoning syntax and domain expertise, and (2) Consistency-Aware Reinforcement Learning to refine deductive reliability. This second stage integrates a novel Logical Consistency Reward, which penalizes logical drift via an option permutation strategy to anchor decisions in verifiable reasoning traces. Experimental results demonstrate that our framework significantly enhances the cognitive reliability and interpretability of RS-VLMs, achieving state-of-the-art performance compared to other advanced methods.

preprint2026arXiv

PILIR: Physics-Informed Local Implicit Representation

Physics-Informed Neural Networks have become a powerful mesh-free method for solving partial differential equations, but their performance is often limited by spectral bias. Specifically, in standard MLPs used in PINNs, the global parameter coupling causes the model to prioritize learning low-frequency components, resulting in slow convergence for high-frequency details. To overcome this limitation, we introduce the Physics-Informed Local Implicit Representation (PILIR). Our approach separates the global physical domain into a discrete latent feature space and a continuous generative decoder. By using a learnable grid to encode explicit spatial locality, PILIR can capture high-frequency details locally, preventing dilution by global patterns. A generative neural operator then synthesizes these local latent features into continuous physical fields, allowing accurate reconstruction of fine-scale structures. Experiments on a range of challenging PDEs show that PILIR effectively mitigates spectral bias, thereby boosting the convergence of high-frequency details and achieving superior accuracy compared to state-of-the-art methods.

preprint2026arXiv

SLGNet: Synergizing Structural Priors and Language-Guided Modulation for Multimodal Object Detection

Multimodal object detection leveraging RGB and Infrared (IR) images is pivotal for robust perception in all-weather scenarios. While recent adapter-based approaches efficiently transfer RGB-pretrained foundation models to this task, they often prioritize model efficiency at the expense of cross-modal structural consistency. Consequently, critical structural cues are frequently lost when significant domain gaps arise, such as in high-contrast or nighttime environments. Moreover, conventional static multimodal fusion mechanisms typically lack environmental awareness, resulting in suboptimal adaptation and constrained detection performance under complex, dynamic scene variations. To address these limitations, we propose SLGNet, a parameter-efficient framework that synergizes hierarchical structural priors and language-guided modulation within a frozen Vision Transformer (ViT)-based foundation model. Specifically, we design a Structure-Aware Adapter to extract hierarchical structural representations from both modalities and dynamically inject them into the ViT to compensate for structural degradation inherent in ViT-based backbones. Furthermore, we propose a Language-Guided Modulation module that exploits VLM-driven structured captions to dynamically recalibrate visual features, thereby endowing the model with robust environmental awareness. Extensive experiments on the LLVIP, FLIR, KAIST, and DroneVehicle datasets demonstrate that SLGNet establishes new state-of-the-art performance. Notably, on the LLVIP benchmark, our method achieves an mAP of 66.1, while reducing trainable parameters by approximately 87% compared to traditional full fine-tuning. This confirms SLGNet as a robust and efficient solution for multimodal perception.

preprint2026arXiv

SRAW-Attack: Space-Reweighted Adversarial Warping Attack for SAR Target Recognition

Synthetic aperture radar (SAR) imagery exhibits intrinsic information sparsity due to its unique electromagnetic scattering mechanism. Despite the widespread adoption of deep neural network (DNN)-based SAR automatic target recognition (SAR-ATR) systems, they remain vulnerable to adversarial examples and tend to over-rely on background regions, leading to degraded adversarial robustness. Existing adversarial attacks for SAR-ATR often require visually perceptible distortions to achieve effective performance, thereby necessitating an attack method that balances effectiveness and stealthiness. In this paper, a novel attack method termed Space-Reweighted Adversarial Warping (SRAW) is proposed, which generates adversarial examples through optimized spatial deformation with reweighted budgets across foreground and background regions. Extensive experiments demonstrate that SRAW significantly degrades the performance of state-of-the-art SAR-ATR models and consistently outperforms existing methods in terms of imperceptibility and adversarial transferability. Code is made available at https://github.com/boremycin/SAR-ATR-TransAttack.

preprint2026arXiv

Video Generation with Predictive Latents

Video Variational Autoencoder (VAE) enables latent video generative modeling by mapping the visual world into compact spatiotemporal latent spaces, improving training efficiency and stability. While existing video VAEs achieve commendable reconstruction quality, continued optimization of reconstruction does not necessarily translate into improved generative performance. How to enhance the diffusability of video latents remains a critical and unresolved challenge. In this work, inspired by principles of predictive world modeling, we investigate the potential of predictive learning to improve the video generative modeling. To this end, we introduce a simple and effective predictive reconstruction objective that unifies predictive learning with video reconstruction. Specifically, we randomly discard future frames and encode only partial past observations, while training the decoder to reconstruct the observed frames and predict future ones simultaneously. This design encourages the latent space to encode temporally predictive structures and build a more coherent understanding of video dynamics, thereby improving generation quality. Our model, termed Predictive Video VAE (PV-VAE), achieves superior performance on video generation, with 52% faster convergence and a 34.42 FVD improvement over the Wan2.2 VAE on UCF101. Furthermore, comprehensive analyses demonstrate that PV-VAE not only exhibits favorable scalability, with generative performance improving alongside VAE training, but also yields consistent gains in downstream video understanding, underscoring a latent space that effectively captures temporal coherence and motion priors.

preprint2025arXiv

Freezing and ice aging dynamics in saline water under natural convection

Understanding the coupled dynamics of liquid-solid phase change and fluid flows is crucial in a wide range of geophysical and industrial applications. When freezing occurs in saline water, the newly formed ice is mushy, with a porous structure that traps the brine within the ice. In this work, which combines experiments and theoretical analyses, we investigate the long-term evolution of saline ice, comprehensively accounting for the coupled dynamics of multiscale fluid flow, heat and mass transfer, and phase change. We show that in a closed convective system the rapid formation of a mushy ice layer is followed by desalination (i.e, the expulsion of salt from the ice) processes that might lead to a slow asymptotic decrease of the ice thickness. Desalination of mushy ice reduces its porosity, which alters the dynamic thermal equilibrium and ice thickness by weakening buoyancy-driven convection within the mushy layer. In turn, changes in brine convection and ice thickness affect the further desalination of the ice. The long-term dynamics of the system can be accurately predicted by a one-dimensional model based on appropriate parameterizations of global heat and mass transfer properties. Furthermore, within the same theoretical model we explore the ice dynamics across a broader parameter space. Our findings advance the understanding of the coupled phase-change physics of saline solutions in the presence of convective fluid flows and provide a basis for explaining and predicting real-world phenomena such as the aging of sea ice.

preprint2025arXiv

Marangoni-driven freezing dynamics of supercooled binary droplets

Solidification of droplets is of great importance to various technological applications, drawing considerable attention from scientists aiming to unravel the fundamental physical mechanisms. In the case of multicomponent droplets undergoing solidification, the emergence of concentration gradients may trigger significant interfacial flows that dominate the freezing dynamics. Here, we experimentally investigate the fascinating interfacial freezing dynamics of supercooled ethanol-water droplets, accompanied with the migration and growth of massive ice particles. We reveal that these unique freezing dynamics are driven by solidification-induced solutal Marangoni flow within the droplets. Our model, which incorporates the temperature- and concentration-dependent properties of the ethanol-water mixture, quantitatively predicts both the migration velocity and the growth rate of the ice particles. The former is determined by the solutal Marangoni flow velocity, while the latter is governed by a balance between the latent heat release and the enhanced thermal dissipation by the Marangoni flow. Moreover, we show that the final wrapping state of droplets can be modulated by the concentration of ethanol. Our findings may pave the way for novel insights into the physicochemical hydrodynamics of multicomponent liquids undergoing phase transitions.

preprint2024arXiv

ClassWise-SAM-Adapter: Parameter Efficient Fine-tuning Adapts Segment Anything to SAR Domain for Semantic Segmentation

In the realm of artificial intelligence, the emergence of foundation models, backed by high computing capabilities and extensive data, has been revolutionary. Segment Anything Model (SAM), built on the Vision Transformer (ViT) model with millions of parameters and vast training dataset SA-1B, excels in various segmentation scenarios relying on its significance of semantic information and generalization ability. Such achievement of visual foundation model stimulates continuous researches on specific downstream tasks in computer vision. The ClassWise-SAM-Adapter (CWSAM) is designed to adapt the high-performing SAM for landcover classification on space-borne Synthetic Aperture Radar (SAR) images. The proposed CWSAM freezes most of SAM's parameters and incorporates lightweight adapters for parameter efficient fine-tuning, and a classwise mask decoder is designed to achieve semantic segmentation task. This adapt-tuning method allows for efficient landcover classification of SAR images, balancing the accuracy with computational demand. In addition, the task specific input module injects low frequency information of SAR images by MLP-based layers to improve the model performance. Compared to conventional state-of-the-art semantic segmentation algorithms by extensive experiments, CWSAM showcases enhanced performance with fewer computing resources, highlighting the potential of leveraging foundational models like SAM for specific downstream tasks in the SAR domain. The source code is available at: https://github.com/xypu98/CWSAM.

preprint2023arXiv

Phason-mediated interlayer exciton diffusion in WS2/WSe2 moiré heterostructure

Moiré potentials in two-dimensional materials have been proven to be of fundamental importance to fully understand the electronic structure of van der Waals heterostructures, from superconductivity to correlated excitonic states. However, understanding how the moiré phonons, so-called phasons, affect the properties of the system still remains an uncharted territory. In this work, we demonstrate how phasons are integral to properly describing and understanding low-temperature interlayer exciton diffusion in WS2/WSe2 heterostructure. We perform photoluminescence (PL) spectroscopy to understand how the coupling between the layers, affected by their relative orientation, impacts the excitonic properties of the system. Samples fabricated with stacking angles of 0° and 60° are investigated taking into account the stacking angle dependence of the two common moiré potential profiles. Additionally, we present spatially and time-resolved exciton diffusion measurements, looking at the photoluminescence emission in a temperature range from 30 K to 250 K. An accurate potential for the two configurations are computed via density functional theory (DFT) calculations. Finally, we perform molecular dynamics simulation in order to visualize the phasons motion, estimating the phason speed at different temperatures, providing novel insights into the mechanics of exciton propagation at low temperatures that cannot be explained within the frame of classical exciton diffusion alone.

preprint2023arXiv

Super Sparse 3D Object Detection

As the perception range of LiDAR expands, LiDAR-based 3D object detection contributes ever-increasingly to the long-range perception in autonomous driving. Mainstream 3D object detectors often build dense feature maps, where the cost is quadratic to the perception range, making them hardly scale up to the long-range settings. To enable efficient long-range detection, we first propose a fully sparse object detector termed FSD. FSD is built upon the general sparse voxel encoder and a novel sparse instance recognition (SIR) module. SIR groups the points into instances and applies highly-efficient instance-wise feature extraction. The instance-wise grouping sidesteps the issue of the center feature missing, which hinders the design of the fully sparse architecture. To further enjoy the benefit of fully sparse characteristic, we leverage temporal information to remove data redundancy and propose a super sparse detector named FSD++. FSD++ first generates residual points, which indicate the point changes between consecutive frames. The residual points, along with a few previous foreground points, form the super sparse input data, greatly reducing data redundancy and computational overhead. We comprehensively analyze our method on the large-scale Waymo Open Dataset, and state-of-the-art performance is reported. To showcase the superiority of our method in long-range detection, we also conduct experiments on Argoverse 2 Dataset, where the perception range ($200m$) is much larger than Waymo Open Dataset ($75m$). Code is open-sourced at https://github.com/tusen-ai/SST.

preprint2023arXiv

Towards A Unified Conformer Structure: from ASR to ASV Task

Transformer has achieved extraordinary performance in Natural Language Processing and Computer Vision tasks thanks to its powerful self-attention mechanism, and its variant Conformer has become a state-of-the-art architecture in the field of Automatic Speech Recognition (ASR). However, the main-stream architecture for Automatic Speaker Verification (ASV) is convolutional Neural Networks, and there is still much room for research on the Conformer based ASV. In this paper, firstly, we modify the Conformer architecture from ASR to ASV with very minor changes. Length-Scaled Attention (LSA) method and Sharpness-Aware Minimizationis (SAM) are adopted to improve model generalization. Experiments conducted on VoxCeleb and CN-Celeb show that our Conformer based ASV achieves competitive performance compared with the popular ECAPA-TDNN. Secondly, inspired by the transfer learning strategy, ASV Conformer is natural to be initialized from the pretrained ASR model. Via parameter transferring, self-attention mechanism could better focus on the relationship between sequence features, brings about 11% relative improvement in EER on test set of VoxCeleb and CN-Celeb, which reveals the potential of Conformer to unify ASV and ASR task. Finally, we provide a runtime in ASV-Subtools to evaluate its inference speed in production scenario. Our code is released at https://github.com/Snowdar/asv-subtools/tree/master/doc/papers/conformer.md.

preprint2022arXiv

A Robust Hot Subdwarfs Identification Method Based on Deep Learning

Hot subdwarf star is a particular type of star that is crucial for studying binary evolution and atmospheric diffusion processes. In recent years, identifying Hot subdwarfs by machine learning methods has become a hot topic, but there are still limitations in automation and accuracy. In this paper, we proposed a robust identification method based on the convolutional neural network (CNN). We first constructed the dataset using the spectral data of LAMOS DR7-V1. We then constructed a hybrid recognition model including an 8-class classification model and a binary classification model. The model achieved an accuracy of 96.17% on the testing set. To further validate the accuracy of the model, we selected 835 Hot subdwarfs that were not involved in the training process from the identified LAMOST catalog (2428, including repeated observations) as the validation set. An accuracy of 96.05% was achieved. On this basis, we used the model to filter and classify all 10,640,255 spectra of LAMOST DR7-V1, and obtained a catalog of 2393 Hot subdwarf candidates, of which 2067 have been confirmed. We found 25 new Hot subdwarfs among the remaining candidates by manual validation. The overall accuracy of the model is 87.42%. Overall, the model presented in this study can effectively identify specific spectra with robust results and high accuracy, and can be further applied to the classification of large-scale spectra and the search of specific targets.

preprint2022arXiv

Adaptive Algorithm for Quantum Amplitude Estimation

Quantum amplitude estimation is a key sub-routine of a number of quantum algorithms with various applications. We propose an adaptive algorithm for interval estimation of amplitudes. The quantum part of the algorithm is based only on Grover's algorithm. The key ingredient is the introduction of an adjustment factor, which adjusts the amplitude of good states such that the amplitude after the adjustment, and the original amplitude, can be estimated without ambiguity in the subsequent step. We show with numerical studies that the proposed algorithm uses a similar number of quantum queries to achieve the same level of precision $ε$ compared to state-of-the-art algorithms, but the classical part, i.e., the non-quantum part, has substantially lower computational complexity. We rigorously prove that the number of oracle queries achieves $O(1/ε)$, i.e., a quadratic speedup over classical Monte Carlo sampling, and the computational complexity of the classical part achieves $O(\log(1/ε))$, both up to a double-logarithmic factor.

preprint2022arXiv

Amplify-and-Forward Relaying for Hierarchical Over-the-Air Computation

This paper studies a hierarchical over-the-air computation (AirComp) network over a large area, in which multiple relays are exploited to facilitate data aggregation from massive WDs. We present a two-phase amplify-and-forward (AF) relaying protocol. In the first phase, the WDs simultaneously send their data to the relays, while in the second phase, the relays amplify the respectively received signals and concurrently forward them to the fusion center (FC) for aggregation. Our objective is to minimize the computational mean squared error (MSE) at the FC, by jointly optimizing the WD transmit coefficients, the relay AF coefficients, and the FC de-noising factor, subject to their individual transmit power constraints. First, we consider the centralized design with global channel state information (CSI), in which the inter-relay signals can be exploited beneficially for data aggregation. In this case, we develop an alternating-optimization-based algorithm to obtain a high-quality solution to the computational MSE minimization problem. Next, to reduce the signaling overhead caused by the centralized design, we consider an alternative decentralized design with partial CSI, in which the relays and the FC make their own decisions by only requiring the channel power gain information across different relays. In this case, the relays and FC need to treat the inter-relay signals as harmful interference or noise. Accordingly, we optimize the transmit coefficients of the WDs associated with each relay, and the relay AF coefficients (together with the FC de-noising factor) in an iterative manner, which can be implemented efficiently in a decentralized way.

preprint2022arXiv

An extended mixed finite element method for elliptic interface problems

In this paper, we propose an extended mixed finite element method for elliptic interface problems. By adding some stabilization terms, we present a mixed approximation form based on Brezzi-Douglas-Marini element space and the piecewise constant function space, and show that the discrete inf-sup constant is independent of how the interface intersects the triangulation. Furthermore, we derive that the optimal convergence holds independent of the location of the interface relative to the mesh. Finally, some numerical examples are presented to verify our theoretical results.

preprint2022arXiv

Charge transfer dynamics in MoSe$_{2}$/hBN/WSe$_{2}$ heterostructures

Ultrafast charge transfer processes provide a facile way to create interlayer excitons in directly contacted transition metal dichalcogenide (TMD) layers. More sophisticated heterostructures composed of TMD/hBN/TMD enable new ways to control interlayer exciton properties and achieve novel exciton phenomena, such as exciton insulators and condensates, where longer lifetimes are desired. In this work, we experimentally study the charge transfer dynamics in a heterostructure composed of a 1 nm thick hBN spacer between MoSe$_{2}$ and WSe$_{2}$ monolayers. We observe the hole transfer from MoSe$_{2}$ to WSe$_{2}$ through the hBN barrier with a time constant of 500 ps, which is over 3 orders of magnitude slower than that between TMD layers without a spacer. Furthermore, we observe strong competition between the interlayer charge transfer and intralayer exciton-exciton annihilation processes at high excitation densities. Our work opens possibilities to understand charge transfer pathways in TMD/hBN/TMD heterostructures for the efficient generation and control of interlayer excitons.

preprint2022arXiv

Communication-Efficient and Privacy-Preserving Feature-based Federated Transfer Learning

Federated learning has attracted growing interest as it preserves the clients' privacy. As a variant of federated learning, federated transfer learning utilizes the knowledge from similar tasks and thus has also been intensively studied. However, due to the limited radio spectrum, the communication efficiency of federated learning via wireless links is critical since some tasks may require thousands of Terabytes of uplink payload. In order to improve the communication efficiency, we in this paper propose the feature-based federated transfer learning as an innovative approach to reduce the uplink payload by more than five orders of magnitude compared to that of existing approaches. We first introduce the system design in which the extracted features and outputs are uploaded instead of parameter updates, and then determine the required payload with this approach and provide comparisons with the existing approaches. Subsequently, we analyze the random shuffling scheme that preserves the clients' privacy. Finally, we evaluate the performance of the proposed learning scheme via experiments on an image classification task to show its effectiveness.

preprint2022arXiv

CP2: Copy-Paste Contrastive Pretraining for Semantic Segmentation

Recent advances in self-supervised contrastive learning yield good image-level representation, which favors classification tasks but usually neglects pixel-level detailed information, leading to unsatisfactory transfer performance to dense prediction tasks such as semantic segmentation. In this work, we propose a pixel-wise contrastive learning method called CP2 (Copy-Paste Contrastive Pretraining), which facilitates both image- and pixel-level representation learning and therefore is more suitable for downstream dense prediction tasks. In detail, we copy-paste a random crop from an image (the foreground) onto different background images and pretrain a semantic segmentation model with the objective of 1) distinguishing the foreground pixels from the background pixels, and 2) identifying the composed images that share the same foreground.Experiments show the strong performance of CP2 in downstream semantic segmentation: By finetuning CP2 pretrained models on PASCAL VOC 2012, we obtain 78.6% mIoU with a ResNet-50 and 79.5% with a ViT-S.

preprint2022arXiv

DePS: An improved deep learning model for de novo peptide sequencing

De novo peptide sequencing from mass spectrometry data is an important method for protein identification. Recently, various deep learning approaches were applied for de novo peptide sequencing and DeepNovoV2 is one of the represetative models. In this study, we proposed an enhanced model, DePS, which can improve the accuracy of de novo peptide sequencing even with missing signal peaks or large number of noisy peaks in tandem mass spectrometry data. It is showed that, for the same test set of DeepNovoV2, the DePS model achieved excellent results of 74.22%, 74.21% and 41.68% for amino acid recall, amino acid precision and peptide recall respectively. Furthermore, the results suggested that DePS outperforms DeepNovoV2 on the cross species dataset.

preprint2022arXiv

Device-Cloud Collaborative Recommendation via Meta Controller

On-device machine learning enables the lightweight deployment of recommendation models in local clients, which reduces the burden of the cloud-based recommenders and simultaneously incorporates more real-time user features. Nevertheless, the cloud-based recommendation in the industry is still very important considering its powerful model capacity and the efficient candidate generation from the billion-scale item pool. Previous attempts to integrate the merits of both paradigms mainly resort to a sequential mechanism, which builds the on-device recommender on top of the cloud-based recommendation. However, such a design is inflexible when user interests dramatically change: the on-device model is stuck by the limited item cache while the cloud-based recommendation based on the large item pool do not respond without the new re-fresh feedback. To overcome this issue, we propose a meta controller to dynamically manage the collaboration between the on-device recommender and the cloud-based recommender, and introduce a novel efficient sample construction from the causal perspective to solve the dataset absence issue of meta controller. On the basis of the counterfactual samples and the extended training, extensive experiments in the industrial recommendation scenarios show the promise of meta controller in the device-cloud collaboration.

preprint2022arXiv

Edge-Cloud Polarization and Collaboration: A Comprehensive Survey for AI

Influenced by the great success of deep learning via cloud computing and the rapid development of edge chips, research in artificial intelligence (AI) has shifted to both of the computing paradigms, i.e., cloud computing and edge computing. In recent years, we have witnessed significant progress in developing more advanced AI models on cloud servers that surpass traditional deep learning models owing to model innovations (e.g., Transformers, Pretrained families), explosion of training data and soaring computing capabilities. However, edge computing, especially edge and cloud collaborative computing, are still in its infancy to announce their success due to the resource-constrained IoT scenarios with very limited algorithms deployed. In this survey, we conduct a systematic review for both cloud and edge AI. Specifically, we are the first to set up the collaborative learning mechanism for cloud and edge modeling with a thorough review of the architectures that enable such mechanism. We also discuss potentials and practical experiences of some on-going advanced edge AI topics including pretraining models, graph neural networks and reinforcement learning. Finally, we discuss the promising directions and challenges in this field.

preprint2022arXiv

Imaging Quantum Interference in Stadium-Shaped Monolayer and Bilayer Graphene Quantum Dots

Experimental realization of graphene-based stadium-shaped quantum dots (QDs) have been few and incompatible with scanned probe microscopy. Yet, direct visualization of electronic states within these QDs is crucial for determining the existence of quantum chaos in these systems. We report the fabrication and characterization of electrostatically defined stadium-shaped QDs in heterostructure devices composed of monolayer graphene (MLG) and bilayer graphene (BLG). To realize a stadium-shaped QD, we utilized the tip of a scanning tunneling microscope to charge defects in a supporting hexagonal boron nitride flake. The stadium states visualized are consistent with tight-binding-based simulations, but lack clear quantum chaos signatures. The absence of quantum chaos features in MLG-based stadium QDs is attributed to the leaky nature of the confinement potential due to Klein tunneling. In contrast, for BLG-based stadium QDs (which have stronger confinement) quantum chaos is precluded by the smooth confinement potential which reduces interference and mixing between states.

preprint2022arXiv

Nature of novel moiré exciton states in WSe$_2$/WS$_2$ heterobilayers

Moiré patterns of transition metal dichalcogenide (TMD) heterobilayers have proven to be an ideal platform to host unusual correlated electronic phases, emerging magnetism, and correlated exciton physics. While the existence of novel moiré excitonic states is established through optical measurements, the microscopic nature of these states is still poorly understood, often relying on empirically fit models. Here, combining large-scale first-principles GW-BSE calculations and micro-reflection spectroscopy, we identify the nature of the exciton resonances in WSe$_2$/WS$_2$ moiré superlattices, discovering a surprisingly rich set of moiré excitons that cannot be even qualitatively captured by prevailing continuum models. Our calculations reveal moiré excitons with distinct characters, including modulated Wannier excitons and previously unindentified intralayer charge-transfer excitons. Signatures of these distinct excitonic characters are confirmed experimentally via the unique carrier-density and magnetic-field dependences of different moiré exciton resonances. Our study highlights the highly non-trivial exciton states that can emerge in TMD moiré superlattices, and suggests novel ways of tuning many-body physics in moiré systems by engineering excited-states with specific spatial characters.

preprint2022arXiv

Optimized Design for IRS-Assisted Integrated Sensing and Communication Systems in Clutter Environments

In this paper, we investigate an intelligent reflecting surface (IRS)-assisted integrated sensing and communication (ISAC) system design in a clutter environment. Assisted by an IRS equipped with a uniform linear array (ULA), a multi-antenna base station (BS) is targeted for communicating with multiple communication users (CUs) and sensing multiple targets simultaneously. We consider the IRS-assisted ISAC design in the case with Type-I or Type-II CUs, where each Type-I and Type-II CU can and cannot cancel the interference from sensing signals, respectively. In particular, we aim to maximize the minimum sensing beampattern gain among multiple targets, by jointly optimizing the BS transmit beamforming vectors and the IRS phase shifting matrix, subject to the signal-to-interference-plus-noise ratio (SINR) constraint for each Type-I/Type-II CU, the interference power constraint per clutter, the transmission power constraint at the BS, and the cross-correlation pattern constraint. Due to the coupling of the BS's transmit design variables and the IRS's phase shifting matrix, the formulated max-min IRS-assisted ISAC design problem in the case with Type-I/Type-II CUs is highly non-convex. As such, we propose an efficient algorithm based on the alternating-optimization and semi-definite relaxation (SDR) techniques. In the case with Type-I CUs, we show that the dedicated sensing signal at the BS is always beneficial to improve the sensing performance. By contrast, the dedicated sensing signal at the BS is not required in the case with Type-II CUs. Numerical results are provided to show that the proposed IRS-assisted ISAC design schemes achieve a significant gain over the existing benchmark schemes.

preprint2022arXiv

Performance evaluation of baseline-dependent averaging based onfull-scale SKA1-LOW simulation

The Square Kilometre Array (SKA) is the largest radio interferometer under construction in the world. Its immense amount of visibility data poses a considerable challenge to the subsequent processing by the science data processor (SDP). Baseline dependent averaging (BDA), which reduces the amount of visibility data based on the baseline distribution of the radio interferometer, has become a focus of SKA SDP development. This paper developed and implemented a full-featured BDA module based on Radio Astronomy Simulation, Calibration and Imaging Library (RASCIL). Simulated observations were then performed with RASCIL based on a full-scale SKA1-LOW configuration. The performance of the BDA was systematically investigated and evaluated based on the simulated data. The experimental results presented that the amount of visibility data is reduced by about 50\% to 85\% for different time intervals ($Δt_{max}$). In addition, different $Δt_{max}$ have a significant effect on the imaging quality. The smaller the $Δt_{max}$, the smaller the degradation of the imaging quality.

preprint2022arXiv

Personalizing Intervened Network for Long-tailed Sequential User Behavior Modeling

In an era of information explosion, recommendation systems play an important role in people's daily life by facilitating content exploration. It is known that user activeness, i.e., number of behaviors, tends to follow a long-tail distribution, where the majority of users are with low activeness. In practice, we observe that tail users suffer from significantly lower-quality recommendation than the head users after joint training. We further identify that a model trained on tail users separately still achieve inferior results due to limited data. Though long-tail distributions are ubiquitous in recommendation systems, improving the recommendation performance on the tail users still remains challenge in both research and industry. Directly applying related methods on long-tail distribution might be at risk of hurting the experience of head users, which is less affordable since a small portion of head users with high activeness contribute a considerate portion of platform revenue. In this paper, we propose a novel approach that significantly improves the recommendation performance of the tail users while achieving at least comparable performance for the head users over the base model. The essence of this approach is a novel Gradient Aggregation technique that learns common knowledge shared by all users into a backbone model, followed by separate plugin prediction networks for the head users and the tail users personalization. As for common knowledge learning, we leverage the backward adjustment from the causality theory for deconfounding the gradient estimation and thus shielding off the backbone training from the confounder, i.e., user activeness. We conduct extensive experiments on two public recommendation benchmark datasets and a large-scale industrial datasets collected from the Alipay platform. Empirical studies validate the rationality and effectiveness of our approach.

preprint2022arXiv

RFI Identification Based On Deep-Learning]{A Robust RFI Identification For Radio Interferometry based on a Convolutional Neural Network

The rapid development of new generation radio interferometers such as the Square Kilometer Array (SKA) has opened up unprecedented opportunities for astronomical research. However, anthropogenic Radio Frequency Interference (RFI) from communication technologies and other human activities severely affects the fidelity of observational data. It also significantly reduces the sensitivity of the telescopes. We proposed a robust Convolutional Neural Network (CNN) model to identify RFI based on machine learning methods. We overlaid RFI on the simulation data of SKA1-LOW to construct three visibility function datasets. One dataset was used for modeling, and the other two were used for validating the model's usability. The experimental results show that the Area Under the Curve (AUC) reaches 0.93, with satisfactory accuracy and precision. We then further investigated the effectiveness of the model by identifying the RFI in the actual observational data from LOFAR and MeerKAT. The results show that the model performs well. The overall effectiveness is comparable to AOFlagger software and provides an improvement over existing methods in some instances.

preprint2022arXiv

Sequential Offloading for Distributed DNN Computation in Multiuser MEC Systems

This paper studies a sequential task offloading problem for a multiuser mobile edge computing (MEC) system. We consider a dynamic optimization approach, which embraces wireless channel fluctuations and random deep neural network (DNN) task arrivals over an infinite horizon. Specifically, we introduce a local CPU workload queue (WD-QSI) and an MEC server workload queue (MEC-QSI) to model the dynamic workload of DNN tasks at each WD and the MEC server, respectively. The transmit power and the partitioning of the local DNN task at each WD are dynamically determined based on the instantaneous channel conditions (to capture the transmission opportunities) and the instantaneous WD-QSI and MEC-QSI (to capture the dynamic urgency of the tasks) to minimize the average latency of the DNN tasks. The joint optimization can be formulated as an ergodic Markov decision process (MDP), in which the optimality condition is characterized by a centralized Bellman equation. However, the brute force solution of the MDP is not viable due to the curse of dimensionality as well as the requirement for knowledge of the global state information. To overcome these issues, we first decompose the MDP into multiple lower dimensional sub-MDPs, each of which can be associated with a WD or the MEC server. Next, we further develop a parametric online Q-learning algorithm, so that each sub-MDP is solved locally at its associated WD or the MEC server. The proposed solution is completely decentralized in the sense that the transmit power for sequential offloading and the DNN task partitioning can be determined based on the local channel state information (CSI) and the local WD-QSI at the WD only. Additionally, no prior knowledge of the distribution of the DNN task arrivals or the channel statistics will be needed for the MEC server.

preprint2022arXiv

SHREC'22 Track: Sketch-Based 3D Shape Retrieval in the Wild

Sketch-based 3D shape retrieval (SBSR) is an important yet challenging task, which has drawn more and more attention in recent years. Existing approaches address the problem in a restricted setting, without appropriately simulating real application scenarios. To mimic the realistic setting, in this track, we adopt large-scale sketches drawn by amateurs of different levels of drawing skills, as well as a variety of 3D shapes including not only CAD models but also models scanned from real objects. We define two SBSR tasks and construct two benchmarks consisting of more than 46,000 CAD models, 1,700 realistic models, and 145,000 sketches in total. Four teams participated in this track and submitted 15 runs for the two tasks, evaluated by 7 commonly-adopted metrics. We hope that, the benchmarks, the comparative results, and the open-sourced evaluation code will foster future research in this direction among the 3D object retrieval community.

preprint2022arXiv

Spectroscopy Signatures of Electron Correlations in a Trilayer Graphene/hBN Moiré Superlattice

ABC-stacked trilayer graphene/hBN moiré superlattice (TLG/hBN) has emerged as a playground for correlated electron physics. We report spectroscopy measurements of dual-gated TLG/hBN using Fourier transformed infrared photocurrent spectroscopy. We observed a strong optical transition between moiré mini-bands that narrows continuously as a bandgap is opened by gating, indicating a reduction of the single particle bandwidth. At half-filling of the valence flat band, a broad absorption peak emerges at ~18 meV, indicating direct optical excitation across an emerging Mott gap. Similar photocurrent spectra are observed in two other correlated insulating states at quarter- and half-filling of the first conduction band. Our findings provide key parameters of the Hubbard model for the understanding of electron correlation in TLG/hBN.

preprint2022arXiv

The Temporal and Spatial Behaviors of CME Occurrence Rate at Different Latitudes

The statistical study of the Coronal Mass Ejections (CMEs) is a hot topic in solar physics. To further reveal the temporal and spatial behaviors of the CMEs at different latitudes and heights, we analyzed the correlation and phase relationships between the occurrence rate of CMEs, the Coronal Brightness Index (CBI), and the 10.7-cm solar radio flux (F10.7). We found that the occurrence rate of the CMEs correlates with CBI relatively stronger at high latitudes (>=60) than at low latitudes (<=50). At low latitudes, the occurrence rate of the CMEs correlates relatively weaker with CBI than F10.7. There is a relatively stronger correlation relationship between CMEs, F10.7, and CBI during Solar Cycle 24(SC24) than Solar Cycle 23 (SC23). During SC23, the high-latitude CME occurrence rate lags behind F10.7 by three months, and during SC24, the low-latitude CME occurrence rate leads to the low-latitude CBI by one month. The correlation coefficient values turn out to be larger when the very faint CMEsare removed from the samples of the CDAW catalog. Based on our results, we may speculate that the source regions of the high/low-latitude CMEs may vary in height, and the process of magnetic energy accumulation and dissipation is from the lower to the upper atmosphere of the Sun. The temporal offsets between different indicators could help us better understand the physical processes responsible for the solar-terrestrial interactions.

preprint2022arXiv

Towards Understanding and Mitigating Audio Adversarial Examples for Speaker Recognition

Speaker recognition systems (SRSs) have recently been shown to be vulnerable to adversarial attacks, raising significant security concerns. In this work, we systematically investigate transformation and adversarial training based defenses for securing SRSs. According to the characteristic of SRSs, we present 22 diverse transformations and thoroughly evaluate them using 7 recent promising adversarial attacks (4 white-box and 3 black-box) on speaker recognition. With careful regard for best practices in defense evaluations, we analyze the strength of transformations to withstand adaptive attacks. We also evaluate and understand their effectiveness against adaptive attacks when combined with adversarial training. Our study provides lots of useful insights and findings, many of them are new or inconsistent with the conclusions in the image and speech recognition domains, e.g., variable and constant bit rate speech compressions have different performance, and some non-differentiable transformations remain effective against current promising evasion techniques which often work well in the image domain. We demonstrate that the proposed novel feature-level transformation combined with adversarial training is rather effective compared to the sole adversarial training in a complete white-box setting, e.g., increasing the accuracy by 13.62% and attack cost by two orders of magnitude, while other transformations do not necessarily improve the overall defense capability. This work sheds further light on the research directions in this field. We also release our evaluation platform SPEAKERGUARD to foster further research.

preprint2022arXiv

WS-Snapshot: An effective algorithm for wide-field and large-scale imaging

The Square Kilometre Array (SKA) is the largest radio interferometer under construction in the world. The high accuracy, wide-field and large size imaging significantly challenge the construction of the Science Data Processor (SDP) of SKA. We propose a hybrid imaging method based on improved W-Stacking and snapshots. The w range is reduced by fitting the snapshot $uv$ plane, thus effectively enhancing the performance of the improved W-Stacking algorithm. We present a detailed implementation of WS-Snapshot. With full-scale SKA1-LOW simulations, we present the imaging performance and imaging quality results for different parameter cases. The results show that the WS-Snapshot method enables more efficient distributed processing and significantly reduces the computational time overhead within an acceptable accuracy range, which would be crucial for subsequent SKA science studies.

preprint2021arXiv

A Catalog of LAMOST Variable Sources Based on Time-domain Photometry of ZTF

The identification and analysis of different variable sources is a hot issue in astrophysical research. The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) spectroscopic survey has accumulated massive spectral data but contains no information about variable sources. Although a few related studies present variable source catalogs for the LAMOST, the studies still have a few deficiencies regarding the type and number of variable sources identified. In this study, we presented a statistical modeling approach to identify variable source candidates. We first crossed the Kepler, Sloan Digital Sky Survey (SDSS), and Zwicky Transient Facility (ZTF) catalogs to obtain light curves data of variable and non-variable sources. The data are then modeled statistically using commonly used variability parameters, respectively. And then, an optimal variable source identification model is determined using the Receiver Operating Characteristic (ROC) curve and four credible evaluation indices such as precision, accuracy, recall, and F1score. Based on this identification model, a catalog of LAMOST variable sources (including 631,769 variable source candidates with a probability greater than 95% and so on) is obtained. To validate the correctness of the catalog, we performed a two-by-two cross-comparison with the GAIA catalog and other published variable source catalogs. We achieved the correct rate ranging from 50% to 100%. Among the 123,756 sources cross-matched, our variable source catalog identifies 85,669 with a correct rate of 69%, which indicates that the variable source catalog presented in this study is credible.

preprint2021arXiv

A two-species competition model with mixed dispersal and free boundaries in time-periodic environment

This paper is concerned with a Lotka-Volterra type competition model with free boundaries in time-periodic environment. One species is assumed to adopt nonlocal dispersal and the other one adopts mixed dispersal, which is a combination of both random dispersal and nonlocal dispersal. We show that this free boundary problem with more general growth functions admits a unique solution defined for all time. A spreading-vanishing dichotomy is obtained and criteria for spreading and vanishing are provided. Moreover, under the weak competition condition we provide the long-time asymptotic behavior of solution when spreading occurs.

preprint2021arXiv

Correlated interlayer exciton insulator in double layers of monolayer WSe2 and moiré WS2/WSe2

Moiré superlattices in van der Waals heterostructures have emerged as a powerful tool for engineering novel quantum phenomena. Here we report the observation of a correlated interlayer exciton insulator in a double-layer heterostructure composed of a WSe2 monolayer and a WS2/WSe2 moiré bilayer that are separated by an ultrathin hexagonal boron nitride (hBN). The moiré WS2/WSe2 bilayer features a Mott insulator state at hole density p/p0 = 1, where p0 corresponds to one hole per moiré lattice site. When electrons are added to the Mott insulator in the WS2/WSe2 moiré bilayer and an equal number of holes are injected into the WSe2 monolayer, a new interlayer exciton insulator emerges with the holes in the WSe2 monolayer and the electrons in the doped Mott insulator bound together through interlayer Coulomb interactions. The excitonic insulator is stable up to a critical hole density of ~ 0.5p0 in the WSe2 monolayer, beyond which the system becomes metallic. Our study highlights the opportunities for realizing novel quantum phases in double-layer moiré systems due to the interplay between the moiré flat band and strong interlayer electron interactions.

preprint2021arXiv

Correlation-Driven Electron-Hole Asymmetry in Graphene Field Effect Devices

Electron-hole asymmetry is a fundamental property in solids that can determine the nature of quantum phase transitions and the regime of operation for devices. The observation of electron-hole asymmetry in graphene and recently in the phase diagram of bilayer graphene has spurred interest into whether it stems from disorder or from fundamental interactions such as correlations. Here, we report an effective new way to access electron-hole asymmetry in 2D materials by directly measuring the quasiparticle self-energy in graphene/Boron Nitride field effect devices. As the chemical potential moves from the hole to the electron doped side, we see an increased strength of electronic correlations manifested by an increase in the band velocity and inverse quasiparticle lifetime. These results suggest that electronic correlations play an intrinsic role in driving electron hole asymmetry in graphene and provide a new insight for asymmetries in more strongly correlated materials.

preprint2021arXiv

Imaging gate-tunable Tomonaga-Luttinger liquids in 1H-MoSe$_2$ mirror twin boundaries

One-dimensional electron systems (1DESs) exhibit properties that are fundamentally different from higher-dimensional systems. For example, electron-electron interactions in 1DESs have been predicted to induce Tomonaga-Luttinger liquid behavior. Naturally-occurring grain boundaries in single-layer semiconducting transition metal dichalcogenides provide 1D conducting channels that have been proposed to host Tomonaga-Luttinger liquids, but charge density wave physics has also been suggested to explain their behavior. Clear identification of the electronic ground state of this system has been hampered by an inability to electrostatically gate such boundaries and thereby tune their charge carrier concentration. Here we present a scanning tunneling microscopy/spectroscopy study of gate-tunable mirror twin boundaries (MTBs) in single-layer 1H-MoSe$_2$ devices. Gating here enables STM spectroscopy to be performed for different MTB electron densities, thus allowing precise characterization of electron-electron interaction effects. Visualization of MTB electronic structure under these conditions allows unambiguous identification of collective density wave excitations having two distinct velocities, in quantitative agreement with the spin-charge separation predicted by finite-length Tomonaga-Luttinger-liquid theory.

preprint2020arXiv

A Hybrid method of accurate classification for Blazars Of Uncertain Type in Fermi LAT Catalogs

Significant progress in the classification of Fermi unassociated sources , has led to an increasing number of blazars are being found. The optical spectrum is effectively used to classify the blazars into two groups such as BL Lacs and flat spectrum radio quasars (FSRQs). However, the accurate classification of the blazars without optical spectrum information, i.e., blazars of uncertain type (BCUs), remains a significant challenge. In this paper, we present a principal component analysis (PCA) and machine learning hybrid blazars classification method. The method, based on the data from Fermi LAT 3FGL Catalog, first used the PCA to extract the primary features of the BCUs and then used a machine learning algorithm to further classify the BCUs. Experimental results indicate that the that the use of PCA algorithms significantly improved the classification. More importantly, comparison with the Fermi LAT 4FGL Catalog, which contains the spectral classification of those BCUs in the Fermi-LAT 3FGL Catalog, reveals that the proposed classification method in the study exhibits higher accuracy than currently established methods; specifically, 151 out of 171 BL Lacs and 19 out of 24 FSRQs are correctly classified.

preprint2020arXiv

Adversarial jamming attacks and defense strategies via adaptive deep reinforcement learning

As the applications of deep reinforcement learning (DRL) in wireless communications grow, sensitivity of DRL based wireless communication strategies against adversarial attacks has started to draw increasing attention. In order to address such sensitivity and alleviate the resulting security concerns, we in this paper consider a victim user that performs DRL-based dynamic channel access, and an attacker that executes DRLbased jamming attacks to disrupt the victim. Hence, both the victim and attacker are DRL agents and can interact with each other, retrain their models, and adapt to opponents' policies. In this setting, we initially develop an adversarial jamming attack policy that aims at minimizing the accuracy of victim's decision making on dynamic channel access. Subsequently, we devise defense strategies against such an attacker, and propose three defense strategies, namely diversified defense with proportional-integral-derivative (PID) control, diversified defense with an imitation attacker, and defense via orthogonal policies. We design these strategies to maximize the attacked victim's accuracy and evaluate their performances.

preprint2020arXiv

An Augmented Regression Model for Tensors with Missing Values

Heterogeneous but complementary sources of data provide an unprecedented opportunity for developing accurate statistical models of systems. Although the existing methods have shown promising results, they are mostly applicable to situations where the system output is measured in its complete form. In reality, however, it may not be feasible to obtain the complete output measurement of a system, which results in observations that contain missing values. This paper introduces a general framework that integrates tensor regression with tensor completion and proposes an efficient optimization framework that alternates between two steps for parameter estimation. Through multiple simulations and a case study, we evaluate the performance of the proposed method. The results indicate the superiority of the proposed method in comparison to a benchmark.

preprint2020arXiv

An end-to-end CNN framework for polarimetric vision tasks based on polarization-parameter-constructing network

Pixel-wise operations between polarimetric images are important for processing polarization information. For the lack of such operations, the polarization information cannot be fully utilized in convolutional neural network(CNN). In this paper, a novel end-to-end CNN framework for polarization vision tasks is proposed, which enables the networks to take full advantage of polarimetric images. The framework consists of two sub-networks: a polarization-parameter-constructing network (PPCN) and a task network. PPCN implements pixel-wise operations between images in the CNN form with 1x1 convolution kernels. It takes raw polarimetric images as input, and outputs polarization-parametric images to task network so as to complete a vison task. By training together, the PPCN can learn to provide the most suitable polarization-parametric images for the task network and the dataset. Taking faster R-CNN as task network, the experimental results show that compared with existing methods, the proposed framework achieves much higher mean-average-precision (mAP) in object detection task

preprint2020arXiv

Convolutional neural network based deep-learning architecture for intraprostatic tumour contouring on PSMA PET images in patients with primary prostate cancer

Accurate delineation of the intraprostatic gross tumour volume (GTV) is a prerequisite for treatment approaches in patients with primary prostate cancer (PCa). Prostate-specific membrane antigen positron emission tomography (PSMA-PET) may outperform MRI in GTV detection. However, visual GTV delineation underlies interobserver heterogeneity and is time consuming. The aim of this study was to develop a convolutional neural network (CNN) for automated segmentation of intraprostatic tumour (GTV-CNN) in PSMA-PET. Methods: The CNN (3D U-Net) was trained on [68Ga]PSMA-PET images of 152 patients from two different institutions and the training labels were generated manually using a validated technique. The CNN was tested on two independent internal (cohort 1: [68Ga]PSMA-PET, n=18 and cohort 2: [18F]PSMA-PET, n=19) and one external (cohort 3: [68Ga]PSMA-PET, n=20) test-datasets. Accordance between manual contours and GTV-CNN was assessed with Dice-Sørensen coefficient (DSC). Sensitivity and specificity were calculated for the two internal test-datasets by using whole-mount histology. Results: Median DSCs for cohorts 1-3 were 0.84 (range: 0.32-0.95), 0.81 (range: 0.28-0.93) and 0.83 (range: 0.32-0.93), respectively. Sensitivities and specificities for GTV-CNN were comparable with manual expert contours: 0.98 and 0.76 (cohort 1) and 1 and 0.57 (cohort 2), respectively. Computation time was around 6 seconds for a standard dataset. Conclusion: The application of a CNN for automated contouring of intraprostatic GTV in [68Ga]PSMA- and [18F]PSMA-PET images resulted in a high concordance with expert contours and in high sensitivities and specificities in comparison with histology reference. This robust, accurate and fast technique may be implemented for treatment concepts in primary PCa. The trained model and the study's source code are available in an open source repository.

preprint2020arXiv

Cooling-Aware Resource Allocation and Load Management for Mobile Edge Computing Systems

Driven by explosive computation demands of Internet of Things (IoT), mobile edge computing (MEC) provides a promising technique to enhance the computation capability for mobile users. In this paper, we propose a joint resource allocation and load management mechanism in an MEC system with wireless power transfer (WPT), by jointly optimizing the transmit power for WPT, the local/edge computing load, the offloading time, and the frequencies of the central processing units (CPUs) at the access point (AP) and the users. To achieve an energy-efficient and sustainable WPT-MEC system, we minimize the total energy consumption of the AP, while meeting computation latency requirements. Cooling energy which is non-negligible, is taken into account in minimizing the energy consumption of the MEC system. By rigorously orchestrating the state-of-the-art optimization techniques, we design an iterative algorithm and obtain the optimal solution in a semi-closed form. Based on the solution, interesting properties and insights are summarized. Extensive numerical tests show that the proposed algorithm can save up to 90.4% the energy of existing benchmarks.

preprint2020arXiv

COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19

Motivation: The coronavirus disease 2019 (COVID-19) caused by a new type of coronavirus has been emerging from China and led to thousands of death globally since December 2019. Despite many groups have engaged in studying the newly emerged virus and searching for the treatment of COVID-19, the understanding of the COVID-19 target-ligand interactions represents a key chal-lenge. Herein, we introduce COVID-19 Docking Server, a web server that predicts the binding modes between COVID-19 targets and the ligands including small molecules, peptides and anti-bodies. Results: Structures of proteins involved in the virus life cycle were collected or constructed based on the homologs of coronavirus, and prepared ready for docking. The meta platform provides a free and interactive tool for the prediction of COVID-19 target-ligand interactions and following drug discovery for COVID-19.

preprint2020arXiv

Frozen Patterns of Impacted Droplets: From Conical Tips to Toroidal Shapes

We report frozen patterns for the water droplets impacting on a cold substrate through fast-speed images. These patterns can be manipulated by several physical parameters (the droplet size, falling height, and substrate temperature), and the scaling analysis has a remarkable agreement with the phase diagram. The observed double-concentric toroidal shape is attributed to the correlation between the impacting dynamics and freezing process, as confirmed by the spatiotemporal evolution of the droplet temperature, the identified timescale associated with the morphology and solidification ($t_{inn}\simeq τ_{sol}$), and the ice front-advection model. These results for frozen patterns provide insight into the complex interplay of the rapid impacting hydrodynamics, the transient heat transfer, and the intricate solidification process.

preprint2020arXiv

High Yield Growth and Doping of Black Phosphorus with Tunable Electronic Properties

Black phosphorus (BP) has recently attracted significant interest due to its unique electronic and optical properties. Doping is an effective strategy to tune a material's electronic structures, however, the direct and controllable growth of BP with a high yield and its doping remain a great challenge. Here we report an efficient short-distance transport (SDT) growth approach and achieve the controlled growth of high quality BP with the highest yield so far, where 98% of the red phosphorus is converted to BP. The doping of BP by As, Sb, Bi, Se and Te are also achieved by this SDT growth approach. Spectroscopic results show that doping systematically changes its electronic structures including band gap, work function, and energy band position. As a result, we have found that the air-stability of doped BP samples (Sb and Te-doped BP) improves compared with pristine BP, due to the downshift of the conduction band minimum with doping. This work develops a new method to grow BP and doped BP with tunable electronic structures and improved stability, and should extend the uses of these class of materials in various areas.

preprint2020arXiv

Joint Optimization of User Association, Subchannel Allocation, and Power Allocation in Multi-cell Multi-association OFDMA Heterogeneous Networks

Heterogeneous network is a novel network architecture proposed in Long-Term-Evolution~(LTE), which highly increases the capacity and coverage compared with the conventional networks. However, in order to provide the best services, appropriate resource management must be applied. In this paper, we consider the joint optimization problem of user association, subchannel allocation, and power allocation for downlink transmission in Multi-cell Multi-association Orthogonal Frequency Division Multiple Access (OFDMA) heterogeneous networks. To solve the optimization problem, we first divide it into two subproblems: 1) user association and subchannel allocation for fixed power allocation; 2) power allocation for fixed user association and subchannel allocation. Subsequently, we obtain a locally optimal solution for the joint optimization problem by solving these two subproblems alternately. For the first subproblem, we derive the globally optimal solution based on graph theory. For the second subproblem, we obtain a Karush-Kuhn-Tucker (KKT) optimal solution by a low complexity algorithm based on the difference of two convex functions approximation (DCA) method. In addition, the multi-antenna receiver case and the proportional fairness case are also discussed. Simulation results demonstrate that the proposed algorithms can significantly enhance the overall network throughput.

preprint2020arXiv

Optimal Energy Allocation and Task Offloading Policy for Wireless Powered Mobile Edge Computing Systems

This paper studies a wireless powered mobile edge computing (MEC) system with fluctuating channels and dynamic task arrivals over time. We jointly optimize the transmission energy allocation at the energy transmitter (ET) for WPT and the task allocation at the user for local computing and offloading over a particular finite horizon, with the objective of minimizing the total transmission energy consumption at the ET while ensuring the user's successful task execution. First, in order to characterize the fundamental performance limit, we consider the offline optimization by assuming that the perfect knowledge of channel state information and task state information (i.e., task arrival timing and amounts) is known a-priori. In this case, we obtain the well-structured optimal solution in a closed form to the energy minimization problem via convex optimization techniques. Next, inspired by the structured offline solutions obtained above, we develop heuristic online designs for the joint energy and task allocation when the knowledge of CSI/TSI is only causally known. Finally, numerical results are provided to show that the proposed joint designs achieve significantly smaller energy consumption than benchmark schemes with only local computing or full offloading at the user, and the proposed heuristic online designs perform close to the optimal offline solutions.

preprint2020arXiv

Real-Time Resource Allocation for Wireless Powered Multiuser Mobile Edge Computing With Energy and Task Causality

This paper considers a wireless powered multiuser mobile edge computing (MEC) system, in which a multi-antenna hybrid access point (AP) wirelessly charges multiple users, and each user relies on the harvested energy to execute computation tasks. We jointly optimize the energy beamforming and remote task execution at the AP, as well as the local computing and task offloading, aiming to minimize the total system energy consumption over a finite time horizon, subject to causality constraints for both energy harvesting and task arrival at the users. In particular, we consider a practical scenario with casual task state information (TSI) and channel state information (CSI), i.e., only the current and previous TSI and CSI are available, but the future TSI and CSI can only be predicted subject to certain errors. To solve this real-time resource allocation problem, we propose an offline-optimization inspired online design approach. First, we consider the offline optimization case by assuming that the TSI and CSI are perfectly known a-priori. In this case, the energy minimization problem corresponds to a convex problem, for which the semi-closed-form optimal solution is obtained via the Lagrange duality method. Next, inspired by the optimal offline solution, we propose a sliding-window based online resource allocation design in practical cases by integrating with the sequential optimization. Finally, numerical results show that the proposed joint wireless powered MEC designs significantly improve the system's energy efficiency, as compared with the benchmark schemes that consider a sliding window of size one or without such joint optimization.

preprint2020arXiv

Robust Automated Photometry Pipeline for Blurred Images

The primary task of the 1.26-m telescope jointly operated by the National Astronomical Observatory and Guangzhou University is photometric observations of the g, r, and i bands. A data processing pipeline system was set up with mature software packages, such as IRAF, SExtractor, and SCAMP, to process approximately 5 GB of observational data automatically every day. However, the success ratio was significantly reduced when processing blurred images owing to telescope tracking error; this, in turn, significantly constrained the output of the telescope. We propose a robust automated photometric pipeline (RAPP) software that can correctly process blurred images. Two key techniques are presented in detail: blurred star enhancement and robust image matching. A series of tests proved that RAPP not only achieves a photometric success ratio and precision comparable to those of IRAF but also significantly reduces the data processing load and improves the efficiency.

preprint2020arXiv

SpellGCN: Incorporating Phonological and Visual Similarities into Language Models for Chinese Spelling Check

Chinese Spelling Check (CSC) is a task to detect and correct spelling errors in Chinese natural language. Existing methods have made attempts to incorporate the similarity knowledge between Chinese characters. However, they take the similarity knowledge as either an external input resource or just heuristic rules. This paper proposes to incorporate phonological and visual similarity knowledge into language models for CSC via a specialized graph convolutional network (SpellGCN). The model builds a graph over the characters, and SpellGCN is learned to map this graph into a set of inter-dependent character classifiers. These classifiers are applied to the representations extracted by another network, such as BERT, enabling the whole network to be end-to-end trainable. Experiments (The dataset and all code for this paper are available at https://github.com/ACL2020SpellGCN/SpellGCN) are conducted on three human-annotated datasets. Our method achieves superior performance against previous models by a large margin.

preprint2020arXiv

Study of Thermal Expansion Coefficients of 2D Materials via Raman Micro-spectroscopy: Revisited

We report a joint study, using Raman micro-spectroscopy and molecular dynamics simulations, on the substrate effect on thermal properties of 2D materials and revisit measurement of thermal expansion coefficient (TEC) of supported 2D film. Graphene is employed as a representative. We find that the out-of-plane coupling between graphene and substrate strongly affects the temperature-dependent vibrational modes and TEC of graphene. Density of states for long-wavelength out-of-plane oscillations is significantly reduced when graphene is supported on an alkane substrate. To account for the contribution of the out-of-plane coupling to TEC, a Raman micro-spectroscopic scheme is developed. The TEC of graphene on octadecyltrichlorosilane substrate is found to be (-0.6+-0.5)*10-6/K at room temperature, which is fundamentally smaller than that of free-standing graphene. Our results shed light on the understanding of the interaction between 2D material and substrate, and offer a general recipe for optical measurement of TEC of a supported 2D film.

preprint2020arXiv

Tunable ferromagnetism at non-integer filling of a moiré superlattice

The flat bands resulting from moiré superlattices in magic-angle twisted bilayer graphene (MATBG) and ABC-trilayer graphene aligned with hexagonal boron nitride (ABC-TLG/hBN) have been shown to give rise to fascinating correlated electron phenomena such as correlated insulators and superconductivity. More recently, orbital magnetism associated with correlated Chern insulators was found in this class of layered structures centered at integer multiples of n0, the density corresponding to one electron per moiré superlattice unit cell. Here we report the experimental observation of ferromagnetism at fractional filling of a flat Chern band in an ABC-TLG/hBN moirésuperlattice. The ferromagnetic state exhibits prominent ferromagnetic hysteresis behavior with large anomalous Hall resistivity in a broad region of densities, centered in the valence miniband at n = -2.3 n0. This ferromagnetism depends very sensitively on the control parameters in the moiré system: not only the magnitude of the anomalous Hall signal, but also the sign of the hysteretic ferromagnetic response can be modulated by tuning the carrier density and displacement field. Our discovery of electrically tunable ferromagnetism in a moiré Chern band at non-integer filling highlights the opportunities for exploring new correlated ferromagnetic states in moiré heterostructures.

preprint2020arXiv

Ultrafast photocurrent and absorption microscopy of few-layer TMD devices isolate rate-limiting dynamics driving fast and efficient photoresponse

Despite inherently poor interlayer conductivity, photodetectors made from few-layer devices of 2D transition metal dichalcogenides (TMDs) such as WSe$_2$ and MoS$_2$ can still yield a desirably fast ($\leq$90 ps) and efficient ($ε$$>$40\%) photoresponse. By combining ultrafast photocurrent (U-PC) and transient absorption (TA) microscopy, the competing electronic escape and recombination rates are unambiguously identified in otherwise complex kinetics. Both the U-PC and TA response of WSe$_2$ yield matching interlayer electronic escape times that accelerate from 1.6 ns to 86 ns with applied $E$-field to predict the maximum device PC-efficiency realized of $\sim$44\%. The slope of the escape rates versus $E$-field suggests out-of-plane electron and hole mobilities of 0.129 and 0.031 cm$^2$/V$s$ respectively. Above $\sim$10$^{11}$ photons/cm$^{2}$ incident flux, defect-assisted Auger scattering greatly decreases efficiency by trapping carriers at vacancy defects. Both TA and PC spectra identify a metal-vacancy sub-gap peak with $\sim$5.6 ns lifetime as a primary trap capturing carriers as they hop between layers. Synchronous TA and U-PC microscopy show the\ net PC collected is modelled by a kinetic rate-law of electronic escape competing against the linear and nonlinear Auger recombination rates. This simple rate-model further predicts the PC-based dynamics, nonlinear amplitude and efficiency, $ε$ over a 10$^5$ range of incident photon flux in few-layer WSe$_2$ and MoS$_2$ devices.

preprint2020arXiv

Uniformly strong convergence of Kähler-Ricci flows on a Fano manifold

In this paper, we study the uniformly strong convergence of Kähler-Ricci flow on a Fano manifold with varied initial metrics and smooth deformation complex structures. As an application, we prove the uniqueness of Kähler-Ricci solitons in sense of diffeomorphism orbits. The result generalizes Tian-Zhu's theorem for the uniqueness of of Kähler-Ricci solitons on a compact complex manifold, and it is also a generalization of Chen-Sun's result of for the uniqueness of of Kähler-Einstein metric orbits.

preprint2019arXiv

Experimental observation of the gate-controlled reversal of the anomalous Hall effect in the intrinsic magnetic topological insulator MnBi2Te4 device

Here we report the reserved anomalous Hall effect (AHE) in the 5-septuple-layer van der Waals device of the intrinsic magnetic topological insulator MnBi2Te4. By employing the top/bottom gate, a negative AHE loop gradually decreases to zero and changes to a reversed sign. The reversed AHE exhibits distinct coercive fields and temperature dependence from the previous AHE. It reaches the maximum inside the gap of the Dirac cone. The newly-seen reversed AHE is attributed to the competition of the intrinsic Berry curvature and the Dirac-gap enhanced extrinsic skew scattering. Its gate-controlled switching contributes a scheme for the topological spin field-effect transistors.

preprint2019arXiv

Optical detection of Mott and generalized Wigner crystal states in WSe2/WS2 moiré superlattices

Moiré superlattices are emerging as a new route for engineering strongly correlated electronic states in two-dimensional van der Waals heterostructures, as recently demonstrated in the correlated insulating and superconducting states in magic-angle twisted bilayer graphene and ABC trilayer graphene/boron nitride moiré superlattices. Transition metal dichalcogenide (TMDC) moiré heterostructures provide another exciting model system to explore correlated quantum phenomena, with the addition of strong light-matter interactions and large spin-orbital coupling. Here we report the optical detection of strongly correlated phases in semiconducting WSe2/WS2 moiré superlattices. Our sensitive optical detection technique reveals a Mott insulator state at one hole per superlattice site (ν = 1), and surprising insulating phases at fractional filling factors ν = 1/3 and 2/3, which we assign to generalized Wigner crystallization on an underlying lattice. Furthermore, the unique spin-valley optical selection rules of TMDC heterostructures allow us to optically create and investigate low-energy spin excited states in the Mott insulator. We reveal an especially slow spin relaxation lifetime of many microseconds in the Mott insulating state, orders-of-magnitude longer than that of charge excitations. Our studies highlight novel correlated physics that can emerge in moiré superlattices beyond graphene.

preprint2019arXiv

Perfect absorption by an atomically thin crystal

Optical absorption is one of fundamental light-matter interactions. In most materials, optical absorption is a weak perturbation to the light. In this regime, absorption and emission are irreversible, incoherent processes due to strong damping. Excitons in monolayer transition metal dichalcogenides, however, interact strongly with light, leading to optical absorption in the non-perturbative regime where coherent re-emission of the light has to be considered. Between the incoherent and coherent limits, we show that a robust critical coupling condition exists, leading to perfect optical absorption. Up to 99.6% absorption is measured in a sub-nanometer thick MoSe2 monolayer placed in front of a mirror. The perfect absorption is controlled by tuning the exciton-phonon, exciton-exciton, and exciton-photon interactions by temperature, pulsed laser excitation, and a movable mirror, respectively. Our work suggests unprecedented opportunities for engineering exciton-light interactions using two-dimensional atomically thin crystals, enabling novel photonic applications including ultrafast light modulators and sensitive optical sensing.

preprint2019arXiv

Periodic variation and phase analysis of grouped solar flare with sunspot activity

Studies on the periodic variation and the phase relationship between different solar activity indicators are useful for understanding the long-term evolution of solar activity cycle. Here we report the statistical analysis of grouped solar flare (GSF) and sunspot number (SN) during the time interval from January 1965 to March 2009. We find that, 1) the significant periodicities of both GSF and SN are related to the differential rotation periodicity, the quasi-biennial oscillation (QBO), and the eleven-year Schwabe cycle (ESC), but the specific values are not absolutely identical; 2) the ESC signal of GSF lags behind that of SN with an average of 7.8 months during the considered time interval, implying that the systematic phase delays between GSF and SN originate from the inter-solar-cycle signal. Our results may provide evidence about the storage of magnetic energy in the corona.

preprint2019arXiv

Resolving spin, valley, and moiré quasi-angular momentum of interlayer excitons in WSe2/WS2 heterostructures

Moiré superlattices provide a powerful way to engineer properties of electrons and excitons in two-dimensional van der Waals heterostructures. The moiré effect can be especially strong for interlayer excitons, where electrons and holes reside in different layers and can be addressed separately. In particular, it was recently proposed that the moiré superlattice potential not only localizes interlayer exciton states at different superlattice positions, but also hosts an emerging moiré quasi-angular momentum (QAM) that periodically switches the optical selection rules for interlayer excitons at different moiré sites. Here we report the observation of multiple interlayer exciton states coexisting in a WSe2/WS2 moiré superlattice and unambiguously determine their spin, valley, and moiré QAM through novel resonant optical pump-probe spectroscopy and photoluminescence excitation spectroscopy. We demonstrate that interlayer excitons localized at different moiré sites can exhibit opposite optical selection rules due to the spatially-varying moiré QAM. Our observation reveals new opportunities to engineer interlayer exciton states and valley physics with moiré superlattices for optoelectronic and valleytronic applications.

preprint2019arXiv

The $ΔI$=2 bands in $^{109}$In: possible antimagnetic rotation

The high-spin structure of $^{109}$In was investigated with the $^{100}$Mo($^{14}$N, 5$n$)$^{109}$In fusion-evaporation reaction at CIAE, Beijing. Eleven new $γ$-rays of $^{109}$In were identified, by which the bandheads of the $ΔI$=2 rotational bands were confirmed. The configurations were assigned with the help of the systematic discussion. Furthermore, the rotational bands are compared with the tilted-axis cranking calculations based on a relativistic mean-field approach. The rotational bands involving the $1p1h$ excitation to the $π$$d_{5/2}$ and $π$$g_{7/2}$ orbitals are suggested as candidates for antimagnetic rotation based on the theoretical results.

preprint2019arXiv

Tunable Correlated Chern Insulator and Ferromagnetism in Trilayer Graphene/Boron Nitride Moiré Superlattice

Studies on two-dimensional electron systems in a strong magnetic field first revealed the quantum Hall (QH) effect, a topological state of matter featuring a finite Chern number (C) and chiral edge states. Haldane later theorized that Chern insulators with integer QH effects could appear in lattice models with complex hopping parameters even at zero magnetic field. The ABC-trilayer graphene/hexagonal boron nitride (TLG/hBN) moiré superlattice provides an attractive platform to explore Chern insulators because it features nearly flat moiré minibands with a valley-dependent electrically tunable Chern number. Here we report the experimental observation of a correlated Chern insulator in a TLG/hBN moiré superlattice. We show that reversing the direction of the applied vertical electric field switches TLG/hBN's moiré minibands between zero and finite Chern numbers, as revealed by dramatic changes in magneto-transport behavior. For topological hole minibands tuned to have a finite Chern number, we focus on 1/4 filling, corresponding to one hole per moiré unit cell. The Hall resistance is well quantized at h/2e2, i.e. C = 2, for |B| > 0.4 T. The correlated Chern insulator is ferromagnetic, exhibiting significant magnetic hysteresis and a large anomalous Hall signal at zero magnetic field. Our discovery of a C = 2 Chern insulator at zero magnetic field should open up exciting opportunities for discovering novel correlated topological states, possibly with novel topological excitations, in nearly flat and topologically nontrivial moiré minibands.

preprint2019arXiv

Visualization of the flat electronic band in twisted bilayer graphene near the magic angle twist

Bilayer graphene was theorized to host a moire miniband with flat dispersion if the layers are stacked at specific twist angles known as the magic angles. Recently, such twisted bilayer graphene (tBLG) with the first magic angle twist was reported to exhibit correlated insulating state and superconductivity, where the presence of the flat miniband in the system is thought to be essential for the emergence of these ordered phases in the transport measurements. Tunneling spectroscopy and electronic compressibility measurements in tBLG have revealed a van Hove singularity that is consistent with the presence of the flat miniband. However, a direct observation of the flat dispersion in the momentum-space of such moire miniband in tBLG is still elusive. Here, we report the visualization of the flat moire miniband by using angle-resolved photoemission spectroscopy with nanoscale resolution (nanoARPES). The high spatial resolution in nanoARPES enabled the measurement of the local electronic structure of the tBLG. We clearly demonstrate the existence of the flat moire band near the charge neutrality for tBLG close to the magic angle at room temperature.

preprint2017arXiv

High Performance Parallel Image Reconstruction for New Vacuum Solar Telescope

Many technologies have been developed to help improve spatial resolution of observational images for ground-based solar telescopes, such as adaptive optics (AO) systems and post-processing reconstruction. As any AO system correction is only partial, it is indispensable to use post-processing reconstruction techniques. In the New Vacuum Solar Telescope (NVST), speckle masking method is used to achieve the diffraction limited resolution of the telescope. Although the method is very promising, the computation is quite intensive, and the amount of data is tremendous, requiring several months to reconstruct observational data of one day on a high-end computer. To accelerate image reconstruction, we parallelize the program package on a high performance cluster. We describe parallel implementation details for several reconstruction procedures. The code is written in C language using Message Passing Interface (MPI) and optimized for parallel processing in a multi-processor environment. We show the excellent performance of parallel implementation, and the whole data processing speed is about 71 times faster than before. Finally, we analyze the scalability of the code to find possible bottlenecks, and propose several ways to further improve the parallel performance. We conclude that the presented program is capable of executing in real-time reconstruction applications at NVST.

preprint2017arXiv

Reply to "Failure to replicate long-range tunable attractions in colloidal system"

An arxiv paper, ref. [1] by Cao et al., claimed that the tunable attraction reported in our ref. [2] could not be detected. Ref. [1] was submitted to Nature in Apr. 2016 as a Comment on our ref. [2]. Our reply in May 2016 responded to ref. [1] and was reviewed by the editor of Nature and an external referee. Ref. [1] was rejected by Nature in Aug. 2016. We provide our reply, which answers all of the criticisms in ref. [1], in Appendix I. The main text contains a brief reply to the main criticisms.

preprint2016arXiv

Community Detection Algorithm Evaluation using Size and Hashtags

Understanding community structure in social media is critical due to its broad applications such as friend recommendations, link predictions and collaborative filtering. However, there is no widely accepted definition of community in literature. Existing work use structure related metrics such as modularity and function related metrics such as ground truth to measure the performance of community detection algorithms, while ignoring an important metric, size of the community. [1] suggests that the size of community with strong ties in social media should be limited to 150. As we discovered in this paper, the majority of the communities obtained by many popular community detection algorithms are either very small or very large. Too small communities don't have practical value and too large communities contain weak connections therefore not stable. In this paper, we compare various community detection algorithms considering the following metrics: size of the communities, coverage of the communities, extended modularity, triangle participation ratio, and user interest in the same community. We also propose a simple clique based algorithm for community detection as a baseline for the comparison. Experimental results show that both our proposed algorithm and the well-accepted disjoint algorithm InfoMap perform well in all the metrics.

preprint2016arXiv

DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM

Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination.

preprint2016arXiv

Effects of Translation-Rotation Coupling on the Displacement Probability Distribution Functions of Boomerang Colloidal Particles

Prior studies have shown that low symmetry particles such as micro-boomerangs exhibit behaviour of Brownian motion rather different from that of high symmetry particles because convenient tracking points (TPs) are usually inconsistent with the center of hydrodynamic stress (CoH) where the translational and rotational motions are decoupled. In this paper we study the effects of the translation-rotation coupling on the displacement probability distribution functions (PDFs) of the boomerang colloid particles with symmetric arms. By tracking the motions of different points on the particle symmetry axis, we show that as the distance between the TP and the CoH is increased, the effects of translation-rotation coupling becomes pronounced, making the short-time 2D PDF for fixed initial orientation to change from elliptical to crescent shape and the angle averaged PDFs from ellipsoidal-particle-like PDF to a shape with a Gaussian top and long displacement tails. We also observed that at long times the PDFs revert to Gaussian. This crescent shape of 2D PDF provides a clear physical picture of the non-zero mean displacements observed in boomerangs particles.

preprint2016arXiv

Electronic Structure, Surface Doping, and Optical Response in Epitaxial WSe2 Thin Films

High quality WSe2 films have been grown on bilayer graphene (BLG) with layer-by-layer control of thickness using molecular beam epitaxy (MBE). The combination of angle-resolved photoemission (ARPES), scanning tunneling microscopy/spectroscopy (STM/STS), and optical absorption measurements reveal the atomic and electronic structures evolution and optical response of WSe2/BLG. We observe that a bilayer of WSe2 is a direct bandgap semiconductor, when integrated in a BLG-based heterostructure, thus shifting the direct-indirect band gap crossover to trilayer WSe2. In the monolayer limit, WSe2 shows a spin-splitting of 475 meV in the valence band at the K point, the largest value observed among all the MX2 (M = Mo, W; X = S, Se) materials. The exciton binding energy of monolayer-WSe2/BLG is found to be 0.21 eV, a value that is orders of magnitude larger than that of conventional 3D semiconductors, yet small as compared to other 2D transition metal dichalcogennides (TMDCs) semiconductors. Finally, our finding regarding the overall modification of the electronic structure by an alkali metal surface electron doping opens a route to further control the electronic properties of TMDCs.

preprint2016arXiv

Frequency shift in high order harmonic generation from isotopic molecules

We report the first experimental observation of frequency shift in high order harmonic generation (HHG) from isotopic molecules H2 and D2 . It is found that harmonics generated from the isotopic molecules exhibit obvious spectral red shift with respect to those from Ar atom. The red shift is further demonstrated to arise from the laser-driven nuclear motion in isotopic molecules. By utilizing the red shift observed in experiment, we successfully retrieve the nuclear vibrations in H2 and D2, which agree well with the theoretical calculations from the time-dependent Schrodinger equation (TDSE) with Non-Born-Oppenheimer approximation. Moreover, we demonstrate that the frequency shift can be manipulated by changing the laser chirp.

preprint2016arXiv

Imaging electrostatically confined Dirac fermions in graphene quantum dots

Electrostatic confinement of charge carriers in graphene is governed by Klein tunneling, a relativistic quantum process in which particle-hole transmutation leads to unusual anisotropic transmission at pn junction boundaries. Reflection and transmission at these novel potential barriers should affect the quantum interference of electronic wavefunctions near these boundaries. Here we report the use of scanning tunneling microscopy (STM) to map the electronic structure of Dirac fermions confined by circular graphene pn junctions. These effective quantum dots were fabricated using a new technique involving local manipulation of defect charge within the insulating substrate beneath a graphene monolayer. Inside such graphene quantum dots we observe energy levels corresponding to quasi-bound states and we spatially visualize the quantum interference patterns of confined electrons. Dirac fermions outside these quantum dots exhibit Friedel oscillation-like behavior. Bolstered with a theoretical model describing relativistic particles in a harmonic oscillator potential, our findings yield new insight into the spatial behavior of electrostatically confined Dirac fermions.

preprint2016arXiv

Low-cost high performance distributed data storage for multi-channel observations

The New Vacuum Solar Telescope (NVST) is a 1-m solar telescope that aims to observe the fine structures in both the photosphere and the chromosphere of the Sun. The observational data acquired simultaneously from one channel for the chromosphere and two channels for the photosphere bring great challenges to the data storage of NVST. The multi-channel instruments of NVST, including scientific cameras and multi-band spectrometers, generate at least 3 terabytes data per day and require high access performance while storing massive short-exposure images. It is worth studying and implementing a storage system for NVST which would balance the data availability, access performance and the cost of development. In this paper, we build a distributed data storage system (DDSS) for NVST and then deeply evaluate the availability of real-time data storage on a distributed computing environment. The experimental results show that two factors, i.e., the number of concurrent read/write and the file size, are critically important for improving the performance of data access on a distributed environment. Referring to these two factors, three strategies for storing FITS files are presented and implemented to ensure the access performance of the DDSS under conditions of multi-host write and read simultaneously. The real applications of the DDSS proves that the system is capable of meeting the requirements of NVST real-time high performance observational data storage. Our study on the DDSS is the first attempt for modern astronomical telescope systems to store real-time observational data on a low-cost distributed system. The research results and corresponding techniques of the DDSS provide a new option for designing real-time massive astronomical data storage system and will be a reference for future astronomical data storage.

preprint2016arXiv

Mobile Instant Video Clip Sharing: Modeling and Enhancing View Experience

With the rapid development of wireless networking and mobile devices, anytime and anywhere data access becomes readily available nowadays. Given the crowdsourced content capturing and sharing, the preferred content length becomes shorter and shorter, even for such multimedia data as video. A representative is Twitter's Vine service, which, mainly targeting mobile users, enables them to create ultra-short video clips and instantly post and share with their followers. In this paper, we present an initial study on this new generation of instant video clip sharing service enabled by mobile platforms and explore the potentials towards its further enhancement. We closely investigate its unique mobile interface, revealing the key differences between Vine-enabled anytime anywhere data access patterns and that of traditional counterparts. We then examine the scheduling policy to maximize the user watching experience as well as the efficiency on the monetary and energy costs. We show that the generic scheduling problem involves two subproblems, namely, pre-fetching scheduling and watch-time download scheduling, and develop effective solutions towards both of them. The superiority of our solution is demonstrated by extensive trace-driven simulations. To the best of our knowledge, this is the first work on modeling and optimizing the instant video clip sharing on mobile devices.

preprint2016arXiv

Nanoscale control of rewriteable doping patterns in pristine graphene/boron nitride heterostructures

Nanoscale control of charge doping in two-dimensional (2D) materials permits the realization of electronic analogs of optical phenomena, relativistic physics at low energies, and technologically promising nanoelectronics. Electrostatic gating and chemical doping are the two most common methods to achieve local control of such doping. However, these approaches suffer from complicated fabrication processes that introduce contamination, change material properties irreversibly, and lack flexible pattern control. Here we demonstrate a clean, simple, and reversible technique that permits writing, reading, and erasing of doping patterns for 2D materials at the nanometer scale. We accomplish this by employing a graphene/boron nitride (BN) heterostructure that is equipped with a bottom gate electrode. By using electron transport and scanning tunneling microscopy (STM), we demonstrate that spatial control of charge doping can be realized with the application of either light or STM tip voltage excitations in conjunction with a gate electric field. Our straightforward and novel technique provides a new path towards on-demand graphene pn junctions and ultra-thin memory devices.

preprint2016arXiv

NVST data archiving system based on fastbit nosql database

The New Vacuum Solar Telescope (NVST) is a 1-meter vacuum solar telescope that aims to observe the fine structures of active regions on the Sun. The main tasks of the NVST are high resolution imaging and spectral observations, including the measurements of the solar magnetic field. The NVST has been collecting more than 20 million FITS files since it began routine observations in 2012 and produces a maximum observational records of 120 thousand files in a day. Given the large amount of files, the effective archiving and retrieval of files becomes a critical and urgent problem. In this study, we implement a new data archiving system for the NVST based on the Fastbit Not Only Structured Query Language (NoSQL) database. Comparing to the relational database (i.e., MySQL; My Structured Query Language), the Fastbit database manifests distinctive advantages on indexing and querying performance. In a large scale database of 40 million records, the multi-field combined query response time of Fastbit database is about 15 times faster and fully meets the requirements of the NVST. Our study brings a new idea for massive astronomical data archiving and would contribute to the design of data management systems for other astronomical telescopes.

preprint2016arXiv

Observation of charge density wave order in 1D mirror twin boundaries of single-layer MoSe2

Properties of two-dimensional transition metal dichalcogenides are highly sensitive to the presence of defects in the crystal structure. A detailed understanding of defect structure may lead to control of material properties through defect engineering. Here we provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries in single-layer MoSe2. Our low-temperature scanning tunneling microscopy/spectroscopy measurements reveal a substantial bandgap of 60 - 140 meV opening at the Fermi level in the otherwise one dimensional metallic structure. We find an energy-dependent periodic modulation in the density of states along the mirror twin boundary, with a wavelength of approximately three lattice constants. The modulations in the density of states above and below the Fermi level are spatially out of phase, consistent with charge density wave order. In addition to the electronic characterization, we determine the atomic structure and bonding configuration of the one-dimensional mirror twin boundary by means of high-resolution non-contact atomic force microscopy. Density functional theory calculations reproduce both the gap opening and the modulations of the density of states.

preprint2016arXiv

Observation of Ultralong Valley Lifetime in WSe2/MoS2 Heterostructures

The valley degree of freedom in two-dimensional (2D) crystals recently emerged as a novel information carrier in addition to spin and charge. The intrinsic valley lifetime in 2D transition metal dichalcoginides (TMD) is expected to be remarkably long due to the unique spin-valley locking behavior, where the inter-valley scattering of electron requires simultaneously a large momentum transfer to the opposite valley and a flip of the electron spin. The experimentally observed valley lifetime in 2D TMDs, however, has been limited to tens of nanoseconds so far. Here we report efficient generation of microsecond-long lived valley polarization in WSe2/MoS2 heterostructures by exploiting the ultrafast charge transfer processes in the heterostructure that efficiently creates resident holes in the WSe2 layer. These valley-polarized holes exhibit near unity valley polarization and ultralong valley lifetime: we observe a valley-polarized hole population lifetime of over 1 us, and a valley depolarization lifetime (i.e. inter-valley scattering lifetime) over 40 us at 10 Kelvin. The near-perfect generation of valley-polarized holes in TMD heterostructures with ultralong valley lifetime, orders of magnitude longer than previous results, opens up new opportunities for novel valleytronics and spintronics applications.

preprint2016arXiv

On the relationship between G-band bright point dynamics and their magnetic field strengths

G-band bright points (GBPs) are regarded as good manifestations of magnetic flux concentrations. We aim to investigate the relationship between the dynamic properties of GBPs and their longitudinal magnetic field strengths. High spatial and temporal resolution observations were recorded simultaneously with G-band filtergrams and Narrow-band Filter Imager (NFI) Stokes I and V images with Hinode /Solar Optical Telescope. The GBPs are identified and tracked in the G-band images automatically, and the corresponding longitudinal magnetic field strength of each GBP is extracted from the calibrated NFI magnetograms by a point-to-point method. After categorizing the GBPs into five groups by their longitudinal magnetic field strengths, we analyze the dynamics of GBPs of each group. The results suggest that with increasing longitudinal magnetic field strengths of GBPs correspond to a decrease in their horizontal velocities and motion ranges as well as by showing more complicated motion paths. This suggests that magnetic elements showing weaker magnetic field strengths prefer to move faster and farther along straighter paths, while stronger ones move more slowly in more erratic paths within a smaller region. The dynamic behaviors of GBPs with different longitudinal magnetic field strengths can be explained by that the stronger flux concentrations withstand the convective flows much better than weaker ones.

preprint2016arXiv

Optical modulators with two-dimensional layered materials

Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that two-dimensional layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this review, we cover the state-of-the-art of optical modulators based on two-dimensional layered materials including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as two-dimensional heterostructures, plasmonic structures, and silicon/fibre integrated structures. We also take a look at future perspectives and discuss the potential of yet relatively unexplored mechanisms such as magneto-optic and acousto-optic modulation.

preprint2016arXiv

Origins of Large Voltage Hysteresis in High Energy-Density Metal Fluoride Lithium-Ion Battery Conversion Electrodes

Metal fluoride and oxides can store multiple lithium-ions through conversion chemistry to enable high energy-density lithium-ion batteries. However, their practical applications have been hindered by an unusually large voltage hysteresis between charge and discharge voltage-profiles and the consequent low energy efficiency (< 80%). The physical origins of such hysteresis are rarely studied and poorly understood. Here we employ in situ X-ray absorption spectroscopy (XAS), transmission electron microscopy (TEM), density-functional-theory (DFT) calculations, and galvanostatic intermittent titration technique (GITT) to first correlate the voltage profile of iron fluoride ($FeF_3$), a representative conversion electrode material, with evolution and spatial distribution of intermediate phases in the electrode. The results reveal that, contrary to conventional belief, the phase evolution in the electrode is symmetrical during discharge and charge. However, the spatial evolution of the electrochemically active phases, which is controlled by reaction kinetics, is different. We further propose that the voltage hysteresis in the $FeF_3$ electrode is kinetic in nature. It is the result of Ohmic voltage drop, reaction overpotential, and different spatial distributions of electrochemically-active phases (i.e. compositional inhomogeneity). Therefore, the large hysteresis can be expected to be mitigated by rational design and optimization of material microstructure and electrode architecture to improve the energy efficiency of lithium-ion batteries based on conversion chemistry.

preprint2016arXiv

Structure of spaces with Bakry-Émery Ricci curvature bounded below

In this paper, we explore the limit structure of a sequence of Riemannian manifolds with Bakry-Émery Ricci curvature bounded below in the Gromov-Hausdorff topology. By extending the techniques established by Cheeger-Cloding for Riemannian manifolds with Ricci curvature bounded below, we prove that each tangent space at a point of the limit space is a metric cone. We also analyze the singular structure of the limit space analogous to a work of Cheeger-Colding-Tian. Our results will be applied to study the limit space of a sequence of Kähler metrics arising from solutions of certain complex Monge-Ampère equations for the existence of Kähler-Ricci solitons on a Fano manifold via the continuity method.

preprint2016arXiv

Survey on the attention based RNN model and its applications in computer vision

The recurrent neural networks (RNN) can be used to solve the sequence to sequence problem, where both the input and the output have sequential structures. Usually there are some implicit relations between the structures. However, it is hard for the common RNN model to fully explore the relations between the sequences. In this survey, we introduce some attention based RNN models which can focus on different parts of the input for each output item, in order to explore and take advantage of the implicit relations between the input and the output items. The different attention mechanisms are described in detail. We then introduce some applications in computer vision which apply the attention based RNN models. The superiority of the attention based RNN model is shown by the experimental results. At last some future research directions are given.

preprint2015arXiv

A reaction-diffusion-advection competition model with two free boundaries in heterogeneous time-periodic environment

In this paper, we study the dynamics of a two-species competition model with two different free boundaries in heterogeneous time-periodic environment, where the two species adopt a combination of random movement and advection upward or downward along the resource gradient. We show that the dynamics of this model can be classified into four cases, which forms a spreading-vanishing quartering. The notion of the minimal habitat size for spreading is introduced to determine if species can always spread. Rough estimates of the asymptotic spreading speed of free boundaries and the long time behavior of solutions are also established when spreading occurs. Furthermore, some sufficient conditions for spreading and vanishing are provided.

preprint2015arXiv

A Review on the Salt Bridge Between ASP177 and ARG163 of Wild-Type Rabbit Prion Protein

Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer, elks, humans and mice etc., but rabbits have a low susceptibility to be infected by prion diseases with respect to other species. The stability of rabbit prion protein is due to its highly ordered β2-α2 loop (PLoS One 5(10) e13273 (2010); Journal of Biological Chemistry 285(41) 31682-31693 (2010)) and a hydrophobic staple helix-capping motif (PNAS 107(46) 19808-19813 (2010); PLoS One 8 (5) e63047 (2013)). The β2-α2 loop and the tail of Helix 3 it interacts with have been a focus in prion protein structure studies. For this loop we found a salt bridge linkage ASP177-ARG163 (O-N) (Journal of Theoretical Biology 342 (7 February 2014) 70-82 (2014)). Some scientists said on the 2FJ3.pdb NMR file of the rabbit prion protein, the distance of ASP177-ARG163 (O-N) gives the salt bridge of about 10 Å which is nearly null in terms of energy and such a salt bridge is not observed in their work. But, from the 3O79.pdb X-ray file of the rabbit prion protein, we can clearly observe this salt bridge. This article analyses the NMR and X-ray structures and gives an answer to the above question: the salt bridge presents at pH 6.5 in the X-ray structure is simply gone at pH 4.5 in the NMR structure is simply due to the different pH values that impact electrostatics at the salt bridge and hence also impact the structures. Moreover, some molecular dynamics simulation results of the X-ray structure are reported in this article to reveal the secrets of the structural stability of rabbit prion protein.

preprint2015arXiv

Amplitude- and phase-resolved nano-spectral imaging of phonon polaritons in hexagonal boron nitride

Phonon polaritons are quasiparticles resulting from strong coupling of photons with optical phonons. Excitation and control of these quasiparticles in 2D materials offer the opportunity to confine and transport light at the nanoscale. Here, we image the phonon polariton (PhP) spectral response in thin hexagonal boron nitride (hBN) crystals as a representative 2D material using amplitude- and phase-resolved near-field interferometry with broadband mid-IR synchrotron radiation. The large spectral bandwidth enables the simultaneous measurement of both out-of-plane (780 cm-1) and in-plane (1370 cm-1) hBN phonon modes. In contrast to the strong and dispersive in-plane mode, the out-of-plane mode PhP response is weak. Measurements of the PhP wavelength reveal a proportional dependence on sample thickness for thin hBN flakes, which can be understood by a general model describing two-dimensional polariton excitation in ultrathin materials.

preprint2015arXiv

Crowdsourced Live Streaming over the Cloud

Empowered by today's rich tools for media generation and distribution, and the convenient Internet access, crowdsourced streaming generalizes the single-source streaming paradigm by including massive contributors for a video channel. It calls a joint optimization along the path from crowdsourcers, through streaming servers, to the end-users to minimize the overall latency. The dynamics of the video sources, together with the globalized request demands and the high computation demand from each sourcer, make crowdsourced live streaming challenging even with powerful support from modern cloud computing. In this paper, we present a generic framework that facilitates a cost-effective cloud service for crowdsourced live streaming. Through adaptively leasing, the cloud servers can be provisioned in a fine granularity to accommodate geo-distributed video crowdsourcers. We present an optimal solution to deal with service migration among cloud instances of diverse lease prices. It also addresses the location impact to the streaming quality. To understand the performance of the proposed strategies in the realworld, we have built a prototype system running over the planetlab and the Amazon/Microsoft Cloud. Our extensive experiments demonstrate that the effectiveness of our solution in terms of deployment cost and streaming quality.

preprint2015arXiv

Direct growth of single- and few-layer MoS2 on h-BN with preferred relative rotation angles

Monolayer molybdenum disulphide (MoS2) is a promising two-dimensional direct-bandgap semiconductor with potential applications in atomically thin and flexible electronics. An attractive insulating substrate or mate for MoS2 (and related materials such as graphene) is hexagonal boron nitride (h-BN). Stacked heterostructures of MoS2 and h-BN have been produced by manual transfer methods, but a more efficient and scalable assembly method is needed. Here we demonstrate the direct growth of single- and few-layer MoS2 on h-BN by chemical vapor deposition (CVD) method, which is scalable with suitably structured substrates. The growth mechanisms for single-layer and few-layer samples are found to be distinct, and for single-layer samples low relative rotation angles (<5 degree) between the MoS2 and h-BN lattices prevail. Moreover, MoS2 directly grown on h-BN maintains its intrinsic 1.89 eV bandgap. Our CVD synthesis method presents an important advancement towards controllable and scalable MoS2 based electronic devices.

preprint2015arXiv

Finite-width Gaussian sum rules for $0^{-+}$ pseudoscalar glueball based on correction from instanton-gluon interference to correlation function

Based on correction from instanton-gluon interference to correlation function, the properties of the $0^{-+}$ pseudoscalar glueball is investigated in a family of finite-width Gaussian sum rules. In the framework of semiclassical expansion for quantum chromodynamics $(\textrm{QCD})$ in the instanton liquid background, the contribution arising from the the interference between instantons and the quantum gluon fields is calculated, and included in the correlation function together with pure-classical contribution from instantons and the perturbative one. The interference contribution is turned to be gauge-invariant, free of infrared divergence, and has a great role to restore the positivity of the spectra of the full correlation function. The negligible contribution from vacuum condensates is excluded in our correlation function to avoid the double counting. Instead of the usual zero-width approximation for the resonances, the usual Breit-Wigner form with a suitable threshold behavior for the spectral function of the finite-width resonances is adopted. A consistency between the subtracted and unsubtracted sum rules is very well justified. The values of the mass, decay width and coupling constants for the $0^{-+}$ resonance in which the glueball fraction is dominant are obtained, and agree with the phenomenological analysis.

preprint2015arXiv

Impact of ionization of ferrocene: EOES of alpha- and beta- electrons and the fingerprint orbital of ferrocenium

Ionization process of ferrocene (Fc) to produce ferrocenium cation (Fc+) has been debated as much as the eclipsed and staggered ferrocene conformers. The present quantum mechanical study reveals that removal of an electron does not apparently affect the geometry and symmetry of the cation, as the geometric changes are < 2% with respect to neutral Fc, but produce the fingerprint orbital 8a1 of Fc+. The excess orbital energy spectrum (EOES) of the α- and β-electrons reveals that the electrons originated from the transition metal Fe in both core and valence shells experience significant energy changes in the cation with respect to the neutral ferrocene counterparts, indicating that the Fe-electrons correlate stronger than electrons from other atoms such as carbons in ferrocene. The EOES also exhibits that the orbital energies of the α-electrons in ferrocenium change more significantly than the β-electrons after one β-electron being ionized with respect to ferrocene. The most significant changes upon ionization are dominated by the Fe-electrons in non-degenerate signature orbitals. That is, 4a1 which is dominated by the Fe 3s orbital, 3a2 by the Fe 3pz orbital and the 8a1 orbital (alpha only) by the Fe 3dz2 (one beta-electron is removed from this orbital). The ΔDFT and ΔSCF calculations yield the IP of 6.90 eV and 6.85 eV, respectively, in excellent agreement to the recent measurements of 6.9 \pn 0.1 eV, suggesting that significant relaxation energy exists whereas electron correlation energies are largely cancelled out. A further dual space analysis (DSA) identifies that the momentum profiles of such the singly occupied fingerprint 8a1 orbital indeed experiences most significant changes in all orbitals of Fc+, again indicates that the electron removal of ferrocene ionization is not from the highest occupied molecular orbital.

preprint2015arXiv

Investigation of intergranular bright points from the New Vacuum Solar Telescope

Six high-resolution TiO-band image sequences from the New Vacuum Solar Telescope (NVST) are used to investigate the properties of intergranular bright points (igBPs). We detect the igBPs using a Laplacian and morphological dilation algorithm (LMD) and track them using a three-dimensional segmentation algorithm automatically, and then investigate the morphologic, photometric and dynamic properties of igBPs, in terms of equivalent diameter, the intensity contrast, lifetime, horizontal velocity, diffusion index, motion range and motion type. The statistical results confirm the previous studies based on G-band or TiO-band igBPs from the other telescopes. It illustrates that the TiO data from the NVST have a stable and reliable quality, which are suitable for studying the igBPs. In addition, our method is feasible to detect and track the igBPs in the TiO data from the NVST. With the aid of the vector magnetograms obtained from the Solar Dynamics Observatory /Helioseismic and Magnetic Imager, the properties of igBPs are found to be influenced by their embedded magnetic environments strongly. The area coverage, the size and the intensity contrast values of igBPs are generally larger in the regions with higher magnetic flux. However, the dynamics of igBPs, including the horizontal velocity, the diffusion index, the ratio of motion range and the index of motion type are generally larger in the regions with lower magnetic flux. It suggests that the absence of strong magnetic fields in the medium makes it possible for the igBPs to look smaller and weaker, diffuse faster, move faster and further in a straighter path.

preprint2015arXiv

Molecular Dynamics Studies on the Buffalo Prion Protein

It was reported that buffalo is a low susceptibility species resisting to prion diseases, which are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species. In molecular structures, TSE neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to reveal the reason why buffalo are resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonance structure of bovine and cattle PrP(124-227); immediately we found for buffalo PrPC(124-227) there are 5 hydrogen bonds at Asn143, but at this position bovine/cattle do not have such hydrogen bonds. Same as that of rabbits, dogs or horses, our molecular dynamics studies also confirmed there is a strong salt bridge ASP178-ARG164 (O-N) keeping the beta2-alpha2 loop linked in buffalo. We also found there is a very strong hydrogen bond SER170-TYR218 linking this loop with the C-terminal end of alpha-helix H3. Other information such as (i) there is a very strong salt bridge HIS187-ARG156 (N-O) linking alpha-helices H2 and H1 (if mutation H187R is made at position 187 then the hydrophobic core of PrPC will be exposed), (ii) at D178, there is a hydrogen bond Y169-D178 and a polar contact R164-D178 for BufPrPC instead of a polar contact Q168-D178 for bovine PrPC, (iii) BufPrPC owns 3-10 helices at 125-127, 152-156 and in the beta2-alpha2 loop respectively, and (iv) in beta2-alpha2 loop there are strong pi-contacts, etc, has been discovered.

preprint2015arXiv

On the transferability of three water models developed by adaptive force matching

Water is perhaps the most simulated liquid. Recently three water models have been developed following the adaptive force matching (AFM) method that provides excellent predictions of water properties with only electronic structure information as a reference. Compared to many other electronic structure based force fields that rely on fairly sophisticated energy expressions, the AFM water models use point-charge based energy expressions that are supported by most popular molecular dynamics packages. An outstanding question regarding simple force fields is whether such force fields provide reasonable transferability outside of their conditions of parameterization. A survey of three AFM water models, B3LYPD-4F, BLYPSP-4F, and WAIL are provided for simulations under conditions ranging from the melting point up to the critical point. By including ice-Ih configurations in the training set, the WAIL potential predicts the melting temperate, TM, of ice-Ih correctly. Without training for ice, BLYPSP-4F underestimates TM by about 15 K. Interestingly, the B3LYPD-4F model gives a TM 14 K too high. The overestimation of TM by B3LYPD-4F mostly likely reflects a deficiency of the B3LYP reference. The BLYPSP-4F model gives the best estimate of the boiling temperature TB and is arguably the best potential for simulating water in the temperature range from TM to TB. None of the three AFM potentials provides a good description of the critical point. Although the B3LYPD-4F model gives the correct critical temperature TC and critical density, there are good reasons to believe the agreement is reached fortuitously. Links to Gromacs input files for the three water models are provided at the end of the paper.

preprint2015arXiv

Shear-Exfoliated Phosphorene for Rechargeable Nanoscale Battery

Discovery of atomically thin black phosphorus (called phosphorene) holds promise to be used as an alternative two-dimensional material to graphene and transition metal dichalcogenides especially as an anode material for lithium-ion batteries (LIBs). However, at present bulk black phosphorus (BP) still suffers from rapid capacity fading that results in poor rechargeable performance. Here, for the first time, we use in situ transmission electron microscopy (TEM) to construct nanoscale phosphorene LIBs and visualize the capacity fading mechanism in thick multilayer phosphorene by real time capturing delithiation-induced structural decomposition that reduces electrical conductivity and thus causes irreversibility of lithiated Li3P phase. We further demonstrate that few-layer phosphorene successfully circumvents the structural decomposition and holds superior structural restorability, even subjected to multi-cycle lithiation/delithiation processes and concomitant huge volume expansion. This finding affords new experimental insights into thickness-dependent lithium diffusion kinetics in phosphorene. Additionally, a scalable liquid-phase shear exfoliation route has been developed to produce high-quality ultrathin (monolayer or few-layer) phosphorene, only by a high-speed shear mixer or even a household kitchen blender with the shear rate threshold, which will pave the way for potential large-scale applications in LIBs once the rechargeable phosphorene nanoscale batteries can be transferred to industrialized enlargement in the future.

preprint2015arXiv

Spectrally resolved spatiotemporal features of quantum paths in high-order harmonic generation

We experimentally disentangle the contributions of different quantum paths in high-order harmonic generation (HHG) from the spectrally and spatially resolved harmonic spectra. By adjusting the laser intensity and focusing position, we simultaneously observe the spectrum splitting, frequency shift and intensity-dependent modulation of harmonic yields both for the short and long paths. Based on the simulations, we discriminate the physical mechanisms of the intensity-dependent modulation of HHG due to the quantum path interference and macroscopic interference effects. Moreover, it is shown that the atomic dipole phases of different quantum paths are encoded in the frequency shift. In turn, it enables us to retrieve the atomic dipole phases and the temporal chirps of different quantum paths from the measured harmonic spectra. This result gives an informative mapping of spatiotemporal and spectral features of quantum paths in HHG.

preprint2015arXiv

The diffusive competition problem with a free boundary in heterogeneous time-periodic environment

In this paper, we consider the diffusive competition problem with a free boundary and sign-changing intrinsic growth rate in heterogeneous time-periodic environment, consisting of an invasive species with density $u$ and a native species with density $v$. We assume that $v$ undergoes diffusion and growth in $R^{N}$ , and $u$ exists initially in a ball $B_{h_0}(0)$, but invades into the environment with spreading front $\{r = h(t)\}$. The effect of the dispersal rate $d_1$, the initial occupying habitat $h_0$, the initial density $u_0$ of invasive species $u$, and the parameter $μ$ (see (1.3)) on the dynamics of this free boundary problem are studied. A spreading-vanishing dichotomy is obtained and some sufficient conditions for the invasive species spreading and vanishing are provided. Moreover, when spreading of $u$ happens, some rough estimates of the spreading speed are also given.

preprint2015arXiv

The diffusive competition problem with a free boundary in strong heterogeneous environment and weak heterogeneous environment

In this paper, we consider the diffusive competition problem consisting of an invasive species with density $u$ and a native species with density $v$. We assume that $v$ undergoes diffusion and growth in $[0, \infty)$, and $u$ exists initially in $[0, h_0)$, but invades into the environment with spreading front ${x=h(t)}$. To understand the effect of the dispersal rate $d_1$, the initial occupying habitat $h_0$, the initial density $u_{0}(x)$ of invasive species $(u)$, and the parameter $μ$ (the ratio of the invasion speed of the free boundary and the invasive species gradient at the expanding front) on the dynamics of this free boundary problem, we divide the heterogeneous environment into two cases: strong heterogeneous environment and weak heterogeneous environment. A spreading-vanishing dichotomy is obtained and some sufficient conditions for the invasive species spreading and vanishing is provided both in the strong heterogenous environment and weak heterogenous environment. Moreover, when spreading of $u$ happens, some rough estimates of the spreading speed are also given.

preprint2014arXiv

A diffusive logistic problem with a free boundary in time-periodic environment: favorable habitat or unfavorable habitat

We study the diffusive logistic equation with a free boundary in timeperiodic environment. To understand the effect of the dispersal rate $d$, the original habitat radius $h_0$, the spreading capability $μ$, and the initial density $u_0$ on the dynamics of the problem, we divide the time-periodic habitat into two cases: favorable habitat and unfavorable habitat. By choosing $d$, $h_0$, $μ$ and $u_0$ as variable parameters, we obtain a spreading-vanishing dichotomy and sharp criteria for the spreading and vanishing in time-periodic environment. We introduce the principal eigenvalue $λ_1(d, α, γ, h(t), T)$ to determine the spreading and vanishing of the invasive species. We prove that if $λ_1(d, α, γ, h_0, T)\leq 0$, the spreading must happen; while if $λ_1(d, α, γ, h_0, T)> 0$, the spreading is also possible. Our results show that the species in the favorable habitat can establish itself if the dispersal rate is slow or the occupying habitat is large. In an unfavorable habitat, the species vanishes if the initial density of the species is small, while survive successfully if the initial value is big. Moreover, when spreading occurs, the asymptotic spreading speed of the free boundary is determined.

preprint2014arXiv

A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins

Prion diseases are invariably fatal neurodegenerative diseases that affect humans and animals. Unlike most other amyloid forming neurodegenerative diseases, these can be highly infectious. Prion diseases occur in a variety of species. They include the fatal human neurodegenerative diseases Creutzfeldt-Jakob Disease (CJD), Fatal Familial Insomnia (FFI), Gerstmann-Straussler-Scheinker syndrome (GSS), Kuru, the bovine spongiform encephalopathy (BSE or 'mad-cow' disease) in cattle, the chronic wasting disease (CWD) in deer and elk, and scrapie in sheep and goats, etc. Transmission across the species barrier to humans, especially in the case of BSE in Europe, CWD in North America, and variant CJDs (vCJDs) in young people of UK, is a major public health concern. Fortunately, scientists reported that the (central) hydrophobic region of prion proteins (PrP) controls the formation of diseased prions. This article gives a detailed survey on PrP hydrophobic region and does molecular dynamics studies of human PrP(110-136) to confirm some findings from the survey. The structural bioinformatics presented in this article can be helpful as a reference in three-dimensional images for laboratory experimental works to study PrP hydrophobic region.

preprint2014arXiv

Bergman Kernels and algebraic structure of limit space for a sequence of almost Kähler-Ricci solitons

In this paper, we give a lower bound of Bergman kernels for a sequence of almost Kähler-Einstein Fano manifolds, or more general, a sequence of Fano manifolds with almost Kähler-Ricci solitons. This generalizes a result by Donaldson-Sun, Tian for Kähler-Einstein manifolds sequence with positive scalar curvature. As an application of our result, we prove that the Gromov-Hausdorff limit of sequence is homomorphic to a log terminal $Q$-Fano variety which admits a Kähler-Ricci soliton on its smooth part.

preprint2014arXiv

Characterising motion types of G-band bright points in the quiet Sun

We study the motions of G band bright points (GBPs) in the quiet Sun to obtain the characteristics of different motion types. A high resolution image sequence taken with the Hinode/Solar Optical Telescope (SOT) is used, and GBPs are automatically tracked by segmenting 3D evolutional structures in a space time cube. After putting the GBPs that do not move during their lifetimes aside, the non stationary GBPs are categorized into three types based on an index of motion type. Most GBPs that move in straight or nearly straight lines are categorized into a straight motion type, a few moving in rotary paths into a rotary motion, and the others fall into a motion type we called erratic. The mean horizontal velocity is 2.18 km/s, 1.63 km/s and 1.33 km/s for straight, erratic and rotary motion type, respectively. We find that a GBP drifts at a higher and constant velocity during its whole life if it moves in a straight line. However, it has a lower and variational velocity if it moves in a rotary path. The diffusive process is ballistic, super and sub diffusion for straight, erratic and rotary motion type, respectively. The corresponding diffusion index and coefficients are 2.13 and 850 km2/s, 1.82 and 331 km2/s, 0.73 and 13 km2/s. In terms of direction of motion, it is homogeneous and isotropical, and usually persists between neighbouring frames, no matter what motion type a GBP belongs to.

preprint2014arXiv

Characterization and manipulation of individual defects in insulating hexagonal boron nitride using scanning tunneling microscopy

Defects play a key role in determining the properties of most materials and, because they tend to be highly localized, characterizing them at the single-defect level is particularly important. Scanning tunneling microscopy (STM) has a history of imaging the electronic structure of individual point defects in conductors, semiconductors, and ultrathin films, but single-defect electronic characterization at the nanometer-scale remains an elusive goal for intrinsic bulk insulators. Here we report the characterization and manipulation of individual native defects in an intrinsic bulk hexagonal boron nitride (BN) insulator via STM. Normally, this would be impossible due to the lack of a conducting drain path for electrical current. We overcome this problem by employing a graphene/BN heterostructure, which exploits graphene's atomically thin nature to allow visualization of defect phenomena in the underlying bulk BN. We observe three different defect structures that we attribute to defects within the bulk insulating boron nitride. Using scanning tunneling spectroscopy (STS), we obtain charge and energy-level information for these BN defect structures. In addition to characterizing such defects, we find that it is also possible to manipulate them through voltage pulses applied to our STM tip.

preprint2014arXiv

Colloquium: Graphene spectroscopy

Spectroscopic studies of electronic phenomena in graphene are reviewed. A variety of methods and techniques are surveyed, from quasiparticle spectroscopies (tunneling, photoemission) to methods probing density and current response (infrared optics, Raman) to scanning probe nanoscopy and ultrafast pump-probe experiments. Vast complimentary information derived from these investigations is shown to highlight unusual properties of Dirac quasiparticles and many-body interaction effects in the physics of graphene.

preprint2014arXiv

Evolution of Interlayer Coupling in Twisted MoS2 Bilayers

Van der Waals (vdW) coupling is emerging as a powerful method to engineer and tailor physical properties of atomically thin two-dimensional (2D) materials. In graphene/graphene and graphene/boron-nitride structures it leads to interesting physical phenomena ranging from new van Hove singularities1-4 and Fermi velocity renormalization5, 6 to unconventional quantum Hall effects7 and Hofstadter's butterfly pattern8-12. 2D transition metal dichalcogenides (TMDCs), another system of predominantly vdW-coupled atomically thin layers13, 14, can also exhibit interesting but different coupling phenomena because TMDCs can be direct or indirect bandgap semiconductors15, 16. Here, we present the first study on the evolution of interlayer coupling with twist angles in as-grown MoS2 bilayers. We find that an indirect bandgap emerges in bilayers with any stacking configuration, but the bandgap size varies appreciably with the twist angle: it shows the largest redshift for AA- and AB-stacked bilayers, and a significantly smaller but constant redshift for all other twist angles. The vibration frequency of the out-of-plane phonon in MoS2 shows similar twist angle dependence. Our observations, together with ab initio calculations, reveal that this evolution of interlayer coupling originates from the repulsive steric effects, which leads to different interlayer separations between the two MoS2 layers in different stacking configurations.

preprint2014arXiv

First-principles study of Carbz-PAHTDDT dye sensitizer and two Carbz-derived dyes for dye sensitized solar cells

Two new carbazole-based organic dye sensitizers are designed and investigated in silico. These dyes are designed through chemical modifications of the conjugated bridge of a reference organic sensitizer known as Carbz-PAHTDDT (S9) dye. The aim of designing these dyes was to reduce the energy gap between their highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and to red-shift their absorption response compared to those of the reference S9 dye sensitizer. This reference dye has a reported promising efficiency when coupled with ferrocene-based electrolyte composition. To investigate geometric and electronic structure, density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were conducted on the new dyes as well as the reference dye. The present study indicated that the long-range correction to the theoretical model in the TD-DFT simulation is important to produce accurate absorption wavelengths.The theoretical studies have shown a reduced HOMO-LUMO gap and red-shifted absorption spectra for both of the new candidate dyes. Such findings suggest that the new dyes are promising and suitable for optoelectronic applications.

preprint2014arXiv

From building blocks of proteins to drugs: A quantum chemical study on structure-property relationships of phenylalanine, tyrosine and dopa

Density functional theory and ab initio methods have been employed to address the impacts of hydroxyl (OH) group substitutions on the physico-chemical properties of levodopa (or L-dopa) against the natural amino acids, phenylalanine and tyrosine. L-dopa, which is an important therapeutic drug for Parkinson's disease, shares structural homology with the amino acids, whose structures differ only by OH substitutions in their phenyl side chains. It is revealed that the backbone geometries of the aromatic molecules do not show apparent OH-dependent differences; however, their other molecular-level properties, such as molecular dipole moment, electronic properties and aromaticity, change significantly. The core binding energy spectra indicate that the atom sites that undergo modifications exhibit large energy shifts, so as to accommodate the changes in the intra-molecular chemical environment of the molecules. The binding energies of the modified C 1s sites in the molecules shift as much as 1.8 eV, whereas the electronic changes in their O 1s spectra happen in the higher energy region (ca. 536 eV). The valence spectra provide enhanced insights on the reactivity and chemical properties of the aromatic molecules. The impacts of OH moieties on the valence spectra are predominantly focussed in the energy band<16 eV, where the frontier molecular orbitals display much reorganization and energy shifts from the amino acids to L-dopa. Of the three molecules, L-dopa also has the least HOMO-LUMO energy gap, which can readily explain its proactivity as a drug compound. Furthermore, the nuclear independent chemical shift calculations suggest that L-dopa also has more aromaticity features than those of the amino acids. The OH groups, therefore, play a more prominent role in shaping the physico-chemical properties of L-dopa, which significantly improve its drug potency.

preprint2014arXiv

Gate-dependent Pseudospin Mixing in Graphene/Boron Nitride Moire Superlattices

Electrons in graphene are described by relativistic Dirac-Weyl spinors with a two-component pseudospin1-12. The unique pseudospin structure of Dirac electrons leads to emerging phenomena such as the massless Dirac cone2, anomalous quantum Hall effect2, 3, and Klein tunneling4, 5 in graphene. The capability to manipulate electron pseudospin is highly desirable for novel graphene electronics, and it requires precise control to differentiate the two graphene sub-lattices at atomic level. Graphene/boron nitride (graphene/BN) Moire superlattice, where a fast sub-lattice oscillation due to B-N atoms is superimposed on the slow Moire period, provides an attractive approach to engineer the electron pseudospin in graphene13-18. This unusual Moire superlattice leads to a spinor potential with unusual hybridization of electron pseudospins, which can be probed directly through infrared spectroscopy because optical transitions are very sensitive to excited state wavefunctions. Here, we perform micro-infrared spectroscopy on graphene/BN heterostructure and demonstrate that the Moire superlattice potential is dominated by a pseudospin-mixing component analogous to a spatially varying pseudomagnetic field. In addition, we show that the spinor potential depends sensitively on the gate-induced carrier concentration in graphene, indicating a strong renormalization of the spinor potential from electron-electron interactions. Our study offers deeper understanding of graphene pseudospin structure under spinor Moire potential, as well as exciting opportunities to control pseudospin in two-dimensional heterostructures for novel electronic and photonic nanodevices.

preprint2014arXiv

Modified Futaki invariant and equivariant Riemann-Roch formula

In this paper, we give a new version of the modified Futaki invariant for a test configuration associated to the soliton action on a Fano manifold. Our version will naturally come from toric test configurations defined by Donaldson for toric manifolds. As an application, we show that the modified $K$-energy is proper for toric invariant Kähler potentials on a toric Fano manifold.

preprint2014arXiv

Molecular dynamics studies on the NMR structures of rabbit prion protein wild-type and mutants: surface electrostatic charge distributions

Prion is a misfolded protein found in mammals that causes infectious diseases of the nervous system in humans and animals. Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer, elk and humans etc. Recent studies have shown that rabbits have a low susceptibility to be infected by prion diseases with respect to other animals including humans. The present study employs molecular dynamics (MD) means to unravel the mechanism of rabbit prion proteins (RaPrPC) based on the recently available rabbit NMR structures (of the wild-type and its two mutants of two surface residues). The electrostatic charge distributions on the protein surface are the focus when analysing the MD trajectories. It is found that we can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrPC; this may be useful for the medicinal treatment of prion diseases.

preprint2014arXiv

Observation of an intrinsic bandgap and Landau level renormalization in graphene/boron-nitride heterostructures

Van der Waals heterostructures formed by assembling different two-dimensional atomic crystals into stacks can lead to many new phenomena and device functionalities. In particular, graphene/boron-nitride heterostructures have emerged as a very promising system for band engineering of graphene. However, the intrinsic value and origin of the bandgap in such heterostructures remain unresolved. Here we report the observation of an intrinsic bandgap in epitaxial graphene/boron-nitride heterostructures with zero crystallographic alignment angle. Magneto-optical spectroscopy provides a direct probe of the Landau level transitions in this system and reveals a bandgap of ~ 38 meV (440 K). Moreover, the Landau level transitions are characterized by effective Fermi velocities with a critical dependence on specific transitions and magnetic field. These findings highlight the important role of many body interactions in determining the fundamental properties of graphene heterostructures.

preprint2014arXiv

Ultrafast Generation of Pseudo-magnetic Field for Valley Excitons in WSe2 Monolayers

A new degree of freedom, the valley pseudospin, emerges in atomically thin two-dimensional transition metal dichalcogenides (MX2) and has attracted great scientific interest. The capability to manipulate the valley pseudospin, in analogy to the control of spin in spintronics, can open up exciting opportunities in valleytronics. Here we demonstrate that an ultrafast and ultrahigh valley pseudomagnetic field can be generated using circularly polarized femtosecond pulses to selectively control the valley degree of freedom in monolayer MX2. Employing ultrafast pump-probe spectroscopy, we observed a pure and valley-selective optical Stark effect in WSe2 monolayers from the non-resonant pump, which instantaneously lift the degeneracy of valley exciton transitions without any dissipation. The strength of the optical Stark effect scales linearly with both the pump intensity and the inverse of pump detuning. An energy splitting more than 10 meV between the K and K_prime valley transitions can be achieved, which corresponds to an effective pseudomagnetic field over 170 Tesla. Our study demonstrates efficient and ultrafast control of the valley excitons with optical light, and opens up the possibility to coherent manipulate the valley polarization for quantum information applications.

preprint2014arXiv

Wide-Gap Semiconducting Graphene from Nitrogen-Seeded SiC

All carbon electronics based on graphene has been an elusive goal. For more than a decade, the inability to produce significant band-gaps in this material has prevented the development of semiconducting graphene. While chemical functionalization was thought to be a route to semiconducting graphene, disorder in the chemical adsorbates, leading to low mobilities, have proved to be a hurdle in its production. We demonstrate a new approach to produce semiconducting graphene that uses a small concentration of covalently bonded surface nitrogen, not as a means to functionalize graphene, but instead as a way to constrain and bend graphene. We demonstrate that a submonolayer concentration of nitrogen on SiC is sufficient to pin epitaxial graphene to the SiC interface as it grows, causing the graphene to buckle. The resulting 3-dimensional modulation of the graphene opens a band-gap greater than 0.7eV in the otherwise continuous metallic graphene sheet.

preprint2013arXiv

A QM/MM molecular dynamic simulation and vibrational spectroscopic study of 6-azaCytidine and cytidine

The conformational and vibrational properties of 6-azaCytidine (6-azaC) and Cytidine (Cyt) have been studied in gas phase and aqueous environment. The two most stable conformers of each molecule have been identified and investigated in more details. The stability order of the two most stable conformers of both molecules is changing going from gas phase to solution. The first solvation shell of both molecules has been studied using QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamic) simulations. The Raman vibrational spectra in gas phase and aqueous solution have been simulated and compared with the available experimental data. The two molecules exhibit certain differences reflected in their spectra as a result of structural and conformational differences.

preprint2013arXiv

A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra

Vibrational optical activity (VOA) spectra, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra, of aliphatic amino acids are simulated using density functional theory (DFT) methods in both gas phase (neutral form) and solution (zwitterionic form), together with their respective infrared (IR) and Raman spectra of the amino acids. The DFT models, which are validated by excellent agreements with the available experimental Raman and ROA spectra of alanine in solution, are employed to study other aliphatic amino acids. The inferred (IR) intensive region (below 2000 cm-1) reveals the signature of alkyl side chains, whereas the Raman intensive region (above 3000 cm-1) contains the information of the functional groups in the amino acids. Furthermore, the chiral carbons of the amino acids (except for glycine) dominate the VCD and ROA spectra in the gas phase, but the methyl group vibrations produce stronger VCD and ROA signals in solution. The C-H related asymmetric vibrations dominate the VOA spectra (i.e., VCD and ROA) > 3000 cm-1 reflecting the side chain structures of the amino acids. Finally the carboxyl and the C(2)H modes of aliphatic amino acids, together with the side chain vibrations, are very active in the VCD/IR and ROA/Raman spectra, which makes such the vibrational spectroscopic methods a very attractive means to study biomolecules.

preprint2013arXiv

Brownian Motion of Boomerang Colloidal Particles

We investigate the Brownian motion of boomerang colloidal particles confined between two glass plates. Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short time faster to long time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to a superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.

preprint2013arXiv

CPMD simulation of Cu2+ -- phenylalanine complex under micro-solvated environment

The study combines DFT calculations and CPMD simulations to investigate the structures of phenylalanine-copper (II) ([Phe-Cu]2+) complexes and the micro-solvation processes. ....It is found that the phenylalanine moiety appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n no less than 2). .... The present CPMD simulations reveal that the maximum coordination of Cu2+ in the presence of the Phe ligand does not exceed four: the oxygen atoms from three water molecules and one carboxyl oxygen atom of Phe. Any excess water molecules will migrate to the second solvation shell. Moreover a unique structural motif is present in the lowest energy complexes, which is recognized to be significant in stabilizing the structures of the complexes. .....

preprint2013arXiv

Docking positrophilic electrons into molecular attractive potential of fluorinated methanes

The present study shows that the positrophilic electrons of a molecule dock into the positron attractive potential region in the annihilation process under the plane-wave approximation. The positron-electron annihilation processes of both polar and non-polar fluorinated methanes (CH4-nFn, n=0, 1,..., 4) are studied under this role. The predicted gamma-ray spectra of these fluorinated methanes agree well with the experiments. It further indicates that the positrophilic electrons of a molecule docking at the negative end of a bond dipole are independent from the molecular dipole moment in the annihilation process.

preprint2013arXiv

Dominance of eclipsed ferrocene conformer in solutions revealed by the IR fingerprint spectral splitting

A combined high-resolution Fourier transform infrared (FTIR) spectra of ferrocene (Fc) and density functional theory (DFT) based quantum mechanical calculations confirmed the dominance of the eclipsed Fc conformer in the fingerprint region of 400-500 cm-1. The IR spectra of Fc were measured in solutions with a number of non-polar solvents such as acetonitrile, dichloromethane, tetrahydrofuran and dioxane. The measurements agree well with the earlier IR spectra of Lippincott and Nelson (1958) as well as the most recent IR spectral measurement in dichloromethane solution of Duhovic and Diaconescu (2013). All experimental measurements in the solutions unambiguously exhibit an IR spectral splitting of ca. 15 cm-1 in the 480-500 cm-1 region. The DFT based B3LYP/m6-31G(d) quantum mechanical calculations using implicit solvent models in this study indicates that only the ground electronic state of the eclipsed (D5h) Fc splits in the IR fingerprint region of ca. 500 cm-1. The IR spectral splitting characterises the centre Fe metal related vibrations of the eclipsed Fc, in agreement with our previous finding in gas phase [Mohammadi et al, 2012]. The present study further suggests that the effects of solvents on the IR spectra of Fc in this region are small and the solvent model effects are also small but the solute molecular density (SMD) model seems to produce the most accurate IR spectrum in the region of 400-600 cm-1 of Fc without scaling the calculated results.

preprint2013arXiv

Gamma-ray spectra of methane in the positron-electron annihilation process

Bound electron contribution to the Doppler-shift of gamma-ray spectra in the positron-electron annihilation process of molecular methane has been studied in gas phase. Two accurate ab initio quantum mechanical schemes, i.e. the delocalized molecular orbital (MO) and the localized natural bond orbital (NBO) schemes, are applied to study the multi-centred methane molecule. The present ab initio calculations of methane indicate that the C-H bonds are polarized with the partial negative charge of -0.36 a.u. on the carbon atom and the partial positive charge of +0.09 a.u. on each of the hydrogen atoms. The positively charged hydrogen atoms produce repulsive Coulomb potentials to a positron. Both the MO and NBO schemes further reveal that the 2a1 electrons of methane, that is, the 2a1 electron component of the C-H bonds rather than the whole C-H bonds of methane, predominates the positron-electron annihilation gamma-ray spectra of the molecule. Electrons of a molecule which are dominant the positron-electron annihilation processes are called positrophilic electrons in the present study. It is further shown that the negative electrostatic potential (ESP) of methane facilitates with the density of the positrophilic 2a1 electrons of methane. Other valence electrons (e.g. 1t2) in the C-H bonds play a minor spectator role in the annihilation process of methane.

preprint2013arXiv

High-throughput Imaging and Spectroscopy of Individual Carbon Nanotubes in Devices with Light Microscopy

Two paramount challenges in carbon nanotube research are achieving chirality-controlled synthesis and understanding chirality-dependent device physics. High-throughput and in-situ chirality and electronic structural characterization of individual carbon nanotubes is crucial for addressing these challenges. Optical imaging and spectroscopy has unparalleled throughput and specificity, but its realization for single nanotubes on substrates or in devices has long been an outstanding challenge. Here we demonstrate video-rate imaging and in-situ spectroscopy of individual carbon nanotubes on various substrates and in functional devices using a novel high-contrast polarization-based optical microscopy. Our technique enables the complete chirality profiling of hundreds of as-grown carbon nanotubes. In addition, we in-situ monitor nanotube electronic structure in active field-effect devices, and observe that high-order nanotube optical resonances are dramatically broadened by electrostatic doping. This unexpected behaviour points to strong interband electron-electron scattering processes that can dominate ultrafast dynamics of excited states in carbon nanotubes.

preprint2013arXiv

Improving the electronic and optical properties of Carbz-PAHTDDT-based dyes through chemical modifications

To investigate geometric and electronic structure, a theoretical study is performed on the Carbz-PAHTDDT (S9) organic dye sensitizer. This dye has a reported promising efficiency when coupled with ferrocene-based electrolyte composition. The present study indicated that the long-range correction to the theoretical model in the time-dependent density functional theory is important to produce accurate absorption wavelengths. In the present study, the chemical structure of the original Carbz-PAHTDDT dye on the π-conjugated bridge is also rationally changed to produce new dyes aiming at enhancing the spectral response as a desirable property of organic dyes in DSSC application. The theoretical studies on the new dyes have shown a significant red-shifting and broadening of their absorption spectra.

preprint2013arXiv

In Silico Design, Extended Molecular Dynamic Simulations and Binding Energy Calculations for a New Series of Dually Acting Inhibitors against EGFR and HER2

Starting from the lead structure we have identified in our previous works, we are extending our insight understanding of its potential inhibitory effect against both EGFR and HER2 receptors. Herein and using extended molecular dynamic simulations and different scoring techniques, we are providing plausible explanations for the observed inhibitory effect. Also, we are comparing the binding mechanism in addition to the dynamics of binding with two other approved inhibitors against EGFR (Lapatinib) and HER2 (SYR). Based on this information, we are also designing and in silico screening new potential inhibitors sharing the same scaffold of the lead structure. We have chosen the best scoring inhibitor for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR. It seems that certain substitution pattern guarantees the binding to the conserved water molecule commonly observed with kinase crystal structures. Also, the new inhibitors seem to form a stable interaction with the mutant strain as a direct consequence of their enhanced ability to form additional interactions with binding site residues.

preprint2013arXiv

In silico investigation of lactone and thiolactone inhibitors in bacterial quorum sensing using molecular modeling

In the present study, the origin of the anti-quorum sensing (QS) activities of several members of a recently synthesized and in vitro tested class of lactone and thiolactone based inhibitors were computationally investigated. Docking and molecular dynamic (MD) simulations and binding free energy calculations were carried out to reveal the exact binding and inhibitory profiles of these compounds. The higher in vitro activity of the lactone series relative to their thiolactone isosteres was verified based on estimating the binding energies, the docking scores and monitoring the stability of the complexes produced in the MD simulations. The strong electrostatic contribution to the binding energies may be responsible for the higher inhibitory activity of the lactone with respect to the thiolactone series. The results of this study help to understand the anti-QS properties of lactone-based inhibitors and provide important information that may assist in the synthesis of novel QS inhibitors.

preprint2013arXiv

Intermolecular interactions and substrate effects for an adamantane monolayer on the Au(111) surface

We study theoretically and experimentally the infrared (IR) spectrum of an adamantane monolayer on a Au(111) surface. Using a new STM-based IR spectroscopy technique (IRSTM) we are able to measure both the nanoscale structure of an adamantane monolayer on Au(111) as well as its infrared spectrum, while DFT-based ab initio calculations allow us to interpret the microscopic vibrational dynamics revealed by our measurements. We find that the IR spectrum of an adamantane monolayer on Au(111) is substantially modified with respect to the gas-phase IR spectrum. The first modification is caused by the adamantane--adamantane interaction due to monolayer packing and it reduces the IR intensity of the 2912 cm$^{-1}$ peak (gas phase) by a factor of 3.5. The second modification originates from the adamantane--gold interaction and it increases the IR intensity of the 2938 cm$^{-1}$ peak (gas phase) by a factor of 2.6, and reduces its frequency by 276 cm$^{-1}$. We expect that the techniques described here can be used for an independent estimate of substrate effects and intermolecular interactions in other diamondoid molecules, and for other metallic substrates.

preprint2013arXiv

Modeling Information Diffusion in Online Social Networks with Partial Differential Equations

Online social networks such as Twitter and Facebook have gained tremendous popularity for information exchange. The availability of unprecedented amounts of digital data has accelerated research on information diffusion in online social networks. However, the mechanism of information spreading in online social networks remains elusive due to the complexity of social interactions and rapid change of online social networks. Much of prior work on information diffusion over online social networks has based on empirical and statistical approaches. The majority of dynamical models arising from information diffusion over online social networks involve ordinary differential equations which only depend on time. In a number of recent papers, the authors propose to use partial differential equations(PDEs) to characterize temporal and spatial patterns of information diffusion over online social networks. Built on intuitive cyber-distances such as friendship hops in online social networks, the reaction-diffusion equations take into account influences from various external out-of-network sources, such as the mainstream media, and provide a new analytic framework to study the interplay of structural and topical influences on information diffusion over online social networks. In this survey, we discuss a number of PDE-based models that are validated with real datasets collected from popular online social networks such as Digg and Twitter. Some new developments including the conservation law of information flow in online social networks and information propagation speeds based on traveling wave solutions are presented to solidify the foundation of the PDE models and highlight the new opportunities and challenges for mathematicians as well as computer scientists and researchers in online social networks.

preprint2013arXiv

Qualitative detection of oil adulteration with machine learning approaches

The study focused on the machine learning analysis approaches to identify the adulteration of 9 kinds of edible oil qualitatively and answered the following three questions: Is the oil sample adulterant? How does it constitute? What is the main ingredient of the adulteration oil? After extracting the high-performance liquid chromatography (HPLC) data on triglyceride from 370 oil samples, we applied the adaptive boosting with multi-class Hamming loss (AdaBoost.MH) to distinguish the oil adulteration in contrast with the support vector machine (SVM). Further, we regarded the adulterant oil and the pure oil samples as ones with multiple labels and with only one label, respectively. Then multi-label AdaBoost.MH and multi-label learning vector quantization (ML-LVQ) model were built to determine the ingredients and their relative ratio in the adulteration oil. The experimental results on six measures show that ML-LVQ achieves better performance than multi-label AdaBoost.MH.

preprint2013arXiv

Reveal of small alkanes and isomers using calculated core and valence binding energy spectra and total momentum cross sections

The present study revealed quantum mechanically that the C1s binding energy spectra of the small alkanes (upto six carbons) provide a clear picture of isomeric chemical shift in linear alkanes and branched isomers, whereas the valence binding energy spectra contain more sensitive information regarding the length of the carbon chains. Total momentum cross sections of the alkanes exhibit the information of the chain length as well as constitutional isomers of the small alkanes. The C1s binding energies of small alkanes (including isomers) are position specific and the terminal carbons have the lowest energies. The length of an alkane chain does not apparently affect the C1s energies so that the terminal carbons (289.11 eV) of pentane are almost the same as those of hexane. The valence binding energy spectra of the alkanes are characterized by inner valence and outer valence regions which are separated by an energy gap at approximately 17 eV. The intensities of the total momentum cross sections of the alkanes are proportional to the number of carbons in the alkane chains whereas the shape of the cross sections in small momentum region of p < 0.5 a.u. indicates their branched isomers.

preprint2013arXiv

Structures of cycloserine and 2-oxazolidinone probed by X-ray photoelectron spectroscopy

The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using core and valence photoelectron spectroscopy and theoretical calculations. Isomerization of the central oxazolidine heterocycle and the addition of an amino group yields cycloserine. Theory correctly predicts the C, N and O 1s core spectra, and additionally we report theoretical natural bond orbital (NBO) charges. The valence ionization energies are also in agreement with theory and previous measurements. Although the lowest binding energy part of the spectra of the two compounds show superficial similarities, analysis of the charge densities of the frontier orbitals indicates substantial reorganization of the wave functions as a result of isomerization. The Highest Occupied Molecular Orbital of CS has leading carbonyl π character with contributions from other heavy atoms in the molecule, while the Highest Occupied Molecular Orbital of 2-oxazolidinone has leading nitrogen, carbon and oxygen pπ character. At laboratory temperatures, CS is predicted to exist mainly as two low energy conformers in the gas phase, separated in energy by 4.6 kJ mol-1, whereas 2-oxazolidinone is present as a single conformer in the gas phase. However the experimental spectra do not provide proof of the presence of these conformers.....

preprint2013arXiv

Systematic Determination of Absolute Absorption Cross-section of Individual Carbon Nanotubes

Determination of optical absorption cross-section is always among the central importance of understanding a material. However its realization on individual nanostructures, such as carbon nanotubes, is experimentally challenging due to the small extinction signal using conventional transmission measurements. Here we develop a technique based on polarization manipulation to enhance the sensitivity of single-nanotube absorption spectroscopy by two-orders of magnitude. We systematically determine absorption cross-section over broad spectral range at single-tube level for more than 50 chirality-defined single-walled nanotubes. Our data reveals chirality-dependent one-dimensional photo-physics through the behaviours of exciton oscillator strength and lifetime. We also establish an empirical formula to predict absorption spectrum of any nanotube, which provides the foundation to determine quantum efficiencies in important photoluminescence and photovoltaic processes.

preprint2013arXiv

The Influence of Ca and Y on the Microstructure and Corrosion Resistance of Vacuum Die Casting AZ91 Alloy

The influence of Ca and Y on the microstructure and corrosion resistance of vacuum die casting AZ91 alloy is investigated using optical microscope, electron scanning microscope, weight-loss test and electrochemical corrosion test. The results indicate that the microstructure of AZ91 alloy can be refined, amount of Mg17Al12 phases is reduced, making Mg17Al12 phases transform from banding to reticular, and stringer Al2Ca phases and block Al2Y phases are formed through adding both Ca and Y. The corrosion resistance of AZ91 magnesium alloy can be increased greatly by adding both Ca and Y. The corrosion rate of AZ91-1.5Ca-1.0Y alloy is dropped to 16.2% of that of AZ91 alloy immersed in 3.5% NaCl aqueous solution for 24 hours. The corrosion current density of AZ91-1.5Ca-1.0Y alloy is dropped by one order of magnitude.

preprint2012arXiv

Delay Sensitive Communications over Cognitive Radio Networks

Supporting the quality of service of unlicensed users in cognitive radio networks is very challenging, mainly due to dynamic resource availability because of the licensed users' activities. In this paper, we study the optimal admission control and channel allocation decisions in cognitive overlay networks in order to support delay sensitive communications of unlicensed users. We formulate it as a Markov decision process problem, and solve it by transforming the original formulation into a stochastic shortest path problem. We then propose a simple heuristic control policy, which includes a threshold-based admission control scheme and and a largest-delay-first channel allocation scheme, and prove the optimality of the largest-delay-first channel allocation scheme. We further propose an improved policy using the rollout algorithm. By comparing the performance of both proposed policies with the upper-bound of the maximum revenue, we show that our policies achieve close-to-optimal performance with low complexities.

preprint2012arXiv

Electrical Control of Plasmon Resonance with Graphene

Surface plasmon, with its unique capability to concentrate light into sub-wavelength volume, has enabled great advances in photon science, ranging from nano-antenna and single-molecule Raman scattering to plasmonic waveguide and metamaterials. In many applications it is desirable to control the surface plasmon resonance in situ with electric field. Graphene, with its unique tunable optical properties, provides an ideal material to integrate with nanometallic structures for realizing such control. Here we demonstrate effective modulation of the plasmon resonance in a model system composed of hybrid graphene-gold nanorod structure. Upon electrical gating the strong optical transitions in graphene can be switched on and off, which leads to significant modulation of both the resonance frequency and quality factor of plasmon resonance in gold nanorods. Hybrid graphene-nanometallic structures, as exemplified by this combination of graphene and gold nanorod, provide a general and powerful way for electrical control of plasmon resonances. It holds promise for novel active optical devices and plasmonic circuits at the deep subwavelength scale.

preprint2012arXiv

Electrical Control of Silicon Photonic Crystal Cavity by Graphene

Efficient conversion of electrical signal to optical signal in nano-photonics enables solid state integration of electronics and photonics. Combination of graphene with photonic crystals is promising for electro-optic modulation. In this paper, we demonstrate that by electrostatic gating a single layer of graphene on top of a photonic crystal cavity, the cavity resonance can be changed significantly. A ~2nm change in the cavity resonance linewidth and almost 400% (6 dB) change in resonance reflectivity is observed. In addition, our analysis shows that a graphene-photonic crystal device can potentially be useful for a high speed, and low power absorptive and refractive modulator, while maintaining a small physical footprint.

preprint2012arXiv

Gamma-ray spectra of hexane in gas phase and liquid phase

Theoretical gamma-ray spectra of molecule hexane have been calculated and compared with the experimental results in both gas (Surko et al, 1997) and liquid (Kerr et al, 1965) phases. The present study reveals that in gas phase not all valence electrons of hexane exhibit the same probability to annihilate a positron. Only the positrophilic electrons in the valence space dominate the gamma-ray spectra, which are in good agreement with the gas phase measurement. When hexane is confined in liquid phase, however, the intermolecular interactions ultimately eliminate the free molecular orientation and selectivity for the positrophilic electrons in the gas phase. As a result, the gamma-ray spectra of hexane become an averaged contribution from all valence electrons, which is again in agreement with liquid phase measurement. The roles of the positrophilic electrons in annihilation process for gas and liquid phases of hexane have been recognized for the first time in the present study.

preprint2011arXiv

Diffusive Logistic Model Towards Predicting Information Diffusion in Online Social Networks

Online social networks have recently become an effective and innovative channel for spreading information and influence among hundreds of millions of end users. Many prior work have carried out empirical studies and proposed diffusion models to understand the information diffusion process in online social networks. However, most of these studies focus on the information diffusion in temporal dimension, that is, how the information propagates over time. Little attempt has been given on understanding information diffusion over both temporal and spatial dimensions. In this paper, we propose a Partial Differential Equation (PDE), specifically, a Diffusive Logistic (DL) equation to model the temporal and spatial characteristics of information diffusion in online social networks. To be more specific, we develop a PDE-based theoretical framework to measure and predict the density of influenced users at a given distance from the original information source after a time period. The density of influenced users over time and distance provides valuable insight on the actual information diffusion process. We present the temporal and spatial patterns in a real dataset collected from Digg social news site, and validate the proposed DL equation in terms of predicting the information diffusion process. Our experiment results show that the DL model is indeed able to characterize and predict the process of information propagation in online social networks. For example, for the most popular news with 24,099 votes in Digg, the average prediction accuracy of DL model over all distances during the first 6 hours is 92.08%. To the best of our knowledge, this paper is the first attempt to use PDE-based model to study the information diffusion process in both temporal and spatial dimensions in online social networks.

preprint2011arXiv

Glass transitions in two-dimensional suspensions of colloidal ellipsoids

We observed a two-step glass transition in monolayers of colloidal ellipsoids by video microscopy. The glass transition in the rotational degree of freedom was at a lower density than that in the translational degree of freedom. Between the two transitions, ellipsoids formed an orientational glass. Approaching the respective glass transitions, the rotational and translational fastest-moving particles in the supercooled liquid moved cooperatively and formed clusters with power-law size distributions. The mean cluster sizes diverge in power law as approaching the glass transitions. The clusters of translational and rotational fastest-moving ellipsoids formed mainly within pseudo-nematic domains, and around the domain boundaries, respectively.

preprint2010arXiv

Drude Conductivity of Dirac Fermions in Graphene

Electrons moving in graphene behave as massless Dirac fermions, and they exhibit fascinating low-frequency electrical transport phenomena. Their dynamic response, however, is little known at frequencies above one terahertz (THz). Such knowledge is important not only for a deeper understanding of the Dirac electron quantum transport, but also for graphene applications in ultrahigh speed THz electronics and IR optoelectronics. In this paper, we report the first measurement of high-frequency conductivity of graphene from THz to mid-IR at different carrier concentrations. The conductivity exhibits Drude-like frequency dependence and increases dramatically at THz frequencies, but its absolute strength is substantially lower than theoretical predictions. This anomalous reduction of free electron oscillator strength is corroborated by corresponding changes in graphene interband transitions, as required by the sum rule. Our surprising observation indicates that many-body effects and Dirac fermion-impurity interactions beyond current transport theories are important for Dirac fermion electrical response in graphene.

preprint2009arXiv

A Tunable Phonon-Exciton Fano System in Bilayer Graphene

Interference between different possible paths lies at the heart of quantum physics. Such interference between coupled discrete and continuum states of a system can profoundly change its interaction with light as seen in Fano resonance. Here we present a unique many-body Fano system composed of a discrete phonon vibration and continuous electron-hole pair transitions in bilayer graphene. Mediated by the electron-phonon interactions, the excited state is described by new quanta of elementary excitations of hybrid phonon-exciton nature. Infrared absorption of the hybrid states exhibit characteristic Fano lineshapes with parameters renormalized by many-body interactions. Remarkably, the Fano resonance in bilayer graphene is continuously tunable through electrical gating. Further control of the phonon-exciton coupling may be achieved with an optical field exploiting the excited state infrared activity. This tunable phonon-exciton system also offers the intriguing possibility of a 'phonon laser' with stimulated phonon amplification generated by population inversion of band-edge electrons.